This article discusses programs that can be used in Microsoft Windows to aid PC users in operating system management. The first section discusses tools used to maintain adequate system performance by aiding stability and security. The second section discusses a variety of tools which improve system functionality.

Stability and Security

Keeping your Windows system secure and running like a well oiled machine requires regular maintenance and judicious use of drive space. Be careful to only run executable files that come from trusted sources, and never keep software that you do not use regularly. Always ensure software does not start at boot unless you wish for it to be running at all times using the vital Microsoft tools mentioned below.

There are at least two recommendations for every utility type except where there is an undisputed best that also happens to be free (or if my experience is limited--there will be updates*). For some of these types of software where every option does almost the same thing, using multiple can be redundant and wasteful. It is an especially bad idea to use two anti-viruses or two VPNs because they may compromise each other. Multiple firewalls will just cause a huge annoyance.

Maintenance

Keep your system clean, drives healthy, and data safe.

Vital Microsoft Tools

The following tools provided by Microsoft are the most important system control tools alongside a file manager for taking care of your system. Regularly examine processes and services and determine whether they start at boot and whether you want them to. You must use all of these to truly have full control over your system. If you want to improve the performance of your computer, using these effectively along with Revo Uninstaller will have a bigger impact than anything else. You should look through every installed application, running process, service, auto-starting process, and scheduled task to make sure nothing is enabled unless you need it.

Windows Task Manager: Examine or kill running tasks, processes, services, and monitor resource usage. This application gives a broad overview; there are other applications for more fine-tuned control.
Process Explorer: A great improvement on task manager's Process tab that shows much more information including how different processes relate to each other. This is the only of these tools not built into Windows, but it can be downloaded from Microsoft.
Resource Monitor: This lists much more in depth performance data than task manager's Performance tab and associates data with individual processes. You can use this to identify troublesome software.
Service Control Manager: Use SCM by running Services.msc. This shows you all services and their states. It shows you more information than the Services tab in task manager and actually allows you to manipulate services. You can start/stop them and make them start automatically with Windows (enable), require manual start, or disable them.
MSConfig: Also lets you enable/disable services in a simpler interface, but there are other options as well. For example, it lets you choose which processes auto-start at boot that are not started by a service. For example, Malwarebytes starts as part of a service, but Bitdefender processes are started automatically without being part of a service.
Windows Task Scheduler: As the name suggests, this software manages scheduled tasks that run at specific times or intervals. Many programs automatically add tasks here so ensure that each one is something you want running. Also use this to set up your own tasks if desired.
Control Panel & Administrative Tools: Browse through all of the things here to see all of the customization and control Microsoft has provided built into Windows. Computer Management―the application found in Administrative Tools―is especially useful because it organizes Service Control Manager, Task Scheduler, Event Viewer, Device Manager, Disk Management and a few other tools in a single convenient interface.
Settings: This is a new application for Windows 10 that brings together some of the most frequently used configuration settings in a simple and easy to use interface. It is not very powerful, but it makes basic configuration more convenient.

Expert Tools:

Registry Editor: The registry is the home for almost all Windows system configuration settings. It is not nearly as intuitive as the other interfaces mentioned above. You should carefully study any option you plan on editing before making any changes.
Command Prompt: This is the default command-line shell for Windows, resembling a DOS environment. It is a vital tool for advanced system control not possible using any of the above graphical interfaces. Batch scripts are extremely useful for automating command-line processes. Essentially anything that can be accomplished using the above tools can also be accomplished in the command-line.

Diagnostic Tools

This software provides information to diagnose the state of your PC.

Event Viewer: This is built into Windows. When something goes wrong, it is logged here. Google what you find here for more information.
BlueScreenView: This is a great tool that does not have to be installed, simply downloaded and run. It is like Event Viewer except that it is specialized to analyze BSOD events.
AIDA64: Previously known as Everest, AIDA64 provides a huge amount of general hardware information.

System Cleaner

Over time your system will accumulate a lot of clutter that should be cleaned. Avoid tuneup software with far-fetched or too good to be true claims that they fix everything. You should not expect a system cleaner to make that much of a difference in performance unless your hard drive is full or you have many registry errors. Complicated tuneup software (such as Iolo, Slimware, TuneUp Utilities, etc.) tries to do many of the things that are accomplished by many of the software tools outlined in this article, but it is significantly inferior to approaching it from many angles with more effective dedicated tools; plus tuneup software that runs around the clock will unnecessarily waste CPU and RAM. Always remember the Unix philosophy: "Do One Thing and Do It Well," simplicity, separation, and modularity are key. I recommend using the other tools mentioned in this article and sticking to a simple system cleaner. These two are very good at that specific task. The inferior alternative built into Windows is known as Disk Cleanup.

CCleaner + CCEnhancer (freeware): Advantages include an attractive and easy to use interface, a variety of features, registry cleaning, and CCEnhancer helps cleaning the junk from many third party programs.
BleachBit (open source): Simple cleaner only that ignores the registry and most third party software, but it seems to do a deeper clean of core programs' mess than CCleaner.

Uninstaller

Proprietary uninstallers leave a mess behind. Use a dedicated uninstaller program to do a better job of keeping your computer free from bloatware. Regularly monitor this list of applications and remove ones that you do not use. The inferior alternative built into Windows is known as Add or Remove Programs.

Revo Uninstaller ($40): Revo Uninstaller cleans all traces of software while uninstalling, unlike when done manually in Windows. Installing software with Revo logs installations to improve its already great capabilities. Other features include a variety of system cleaner options.
Comodo Programs Manager (freeware): Manage drivers, services, and Windows features and updates. Comodo mainly organizes tasks already doable in Windows. If you allow it to monitor installations, it can uninstall similarly to Revo. Warning: starts at boot and runs in background at all times unless disabled manually.

Drive management

Manage partitions and keep your disks healthy. Find and repair bad sectors, file system errors, and keep drives aligned properly. The inferior alternative built into Windows is known as Disk Management. I have selected two applications that I personally like, but there are many options here, and most of them are sufficient.

Paragon Hard Disk Manager ($50 - $100 Suite vs Pro). Advantages include a wide variety of features normally covered by dedicated pieces of software such as data backup and recovery, virtual drive management, and drive cloning.
AOMEI Partition Assistant Standard (freeware). Disk and partition management is comparable to Paragon, but it has little as far as extra features go. EaseUS is supposed to have a comparable partition manager, but it has not been tested.

Backup & Recovery

Keep your data safe in the event of drive failures. The inferior alternative built into Windows is known as Backup and Restore.

Acronis True Image ($50): This is a great backup & recovery suite that does everything you would need for data backup. Its incremental backups are especially practical to keep a backup up to date without wasting huge amounts of time on each backup.
EaseUS Data Recovery Wizard (free, $70 or $100): This is a nice recovery suite. Rather than focusing on proactive backups, this software is a last resort to pick find deleted files even on unrecognizable or reformatted partitions.
Piriform Recuva (freeware): This is a great free tool similar to EaseUS. It is limited in comparison to the the paid version.
TestDisk & PhotoRec (open source): Said to be the best free recovery software, but no GUI. Command-line only.

Disk Defragmenter

Only defragment HDDs. There are many third party applications that do a better job than Windows. The inferior alternative built into Windows is known as Disk Defragmenter.

Diskeeper 12 ($30 - $65, Home vs Pro) Many features for active fragmentation management and avoidance. Diskeeper 12 brings new features unseen in 11 to help manage SSDs, but you should be careful regardless because software like this still tends to over-manage SSDs. SSDs are good at managing themselves. Warning: starts at boot and runs in background at all times unless disabled manually.
Puran Defrag (freeware): Despite the archaic looking website, this software features the best capabilities that can be found in any free defragmentation software. Warning: May start at boot and run in background.

Security

Lightweight but effective security software is key for keeping your PC both performing well and free from attacks.

Web Browser Security

The most important method of ensuring you are browsing the web safely is avoiding malicious content altogether. Anti-malware software is not perfect and should only be the last line of defense after many other layers of security.

Javascript & Plugin settings: For the safest possible browser experience, ensure that javascript is disabled (you can whitelist individual websites as you browse the web) and set plugins to "click to play." Javascript and plugins are the easiest way for a website to exploit browser weaknesses and attack your PC without requiring you to do anything except visit the web page.

The following are all free web browser extensions. Either it is available for both Chrome and Firefox, or there are two recommendations--one for each browser. Using all of these together will provide the highest degree of security, but it is not necessary. If you have limited system resources, use discretion to avoid unnecessary redundancy. For example, Ghostery blocks most of what ScriptBlock does, and Scriptblock blocks most of what Ghostery does. ScriptBlock more effectively prevents malicious exploits, whereas Ghostery does not impinge on the functionality of websites as much. Carefully examine every option.

ScriptBlock (Chrome) or NoScript (Firefox): These go beyond just blocking JS and plugins while also giving you a much higher degree of customization than the above settings. They selectively block specific types of scripts based on your settings. You can now whitelist pages in browser settings to improve functionality while still maintaining a high degree of security. This can be very helpful if you frequently visit websites that you do not trust. These extensions are very powerful and can be used without using the above security settings if you would prefer not to have to adjust things twice for every website. They can be used in conjunction with the above settings for absolute overkill security, but it may also cause some frustration to the user. It is worth mentioning that there is an extension called ScriptSafe for Chrome (previously known as ScriptNo). This extension attempts to copy NoScript, and likewise has more users than ScriptBlock, but testing has revealed it is objectively not as good as ScriptBlock or NoScript at blocking scripts.
WOT: This extension provides a safety rating of every website you visit and allows you to read and write reviews. If you try to visit a poorly rated website it will warn you before granting access. This extension puts a logo with varying colors based on the rating of a website next to every Google search result.
Ghostery: This works similarly to an ad blocker, but instead of blocking visible advertisements, it blocks invisible tracking scripts. It is much more privacy oriented than an ad blocker. An alternative is Disconnect, but in my testing it is slightly less effective at discovering tracking scripts.
HTTPS Everywhere: This extension ensures that you always use SSL if it is available, and asks permission before running insecure scripts in an SSL page.
uBlock Origin: Do not use AdBlock or Adblock Plus, they are scams. They are paid by advertisers to let ads through. This is corrupt and reprehensible, analogous to software coming with built in adware. Also do not use uBlock—it is (basically) an impostor of uBlock Origin. If you want to support websites you like by clicking their ads, you can tell uBlock Origin to let them through for specific domains or pages. uBlock is a highly customizable ad blocker with an intuitive element blocker built in.
EditThisCookie: This is a cookie manager that lets you edit or block either specific cookies or all cookies from a domain. This is the newest addition to the list so there is no FF alternative listed--it is only available on Chrome and Opera.
Avast Online Security or Avira Browser Security: These extensions combine what WOT and Ghostery do. I recommend using WOT and Ghostery over either of these, but if WOT and Ghostery are to be avoided for whatever reason, one of these two are suitable alternatives. They are somewhat successful, but Ghostery universally recognizes and blocks more plus it has far more options. Avast does not make it clear what it is blocking and only gives a number. Avira does and lets you choose what to block. WOT also has a much better rating system because it allows you to read and write comments. Avast simply gives you a good/bad rating and the ability to do a good/bad vote. Avira doesn't let you vote at all. The benefit to these is first of all that you can do it all with just one extension, plus Avast claims to do malware scans of websites. One extension that I recommend against is "AVG Do Not Track." AVG only does what Ghostery does, but it does a considerably worse job than even Avast and Avira at that. (update July 2015: most antivirus software now has equivalent versions of these and the same information applies to most of them, but I have not extensively tested them all. Supposedly some do actual virus scans on pages, so that may come in handy, especially if used in conjunction with the actual anti-virus software.)

Firewall

Employing a firewall to block undesired connections (both incoming and outgoing) is a great way to neutralize attack vectors and stifle malicious code. Windows has a strong firewall, however its interface is complex and it takes a long time to configure. Use a third party controller to make configuring your firewall a snap.

Windows Firewall Controller:

Tinywall (freeware): Minimalist context-menu-based interface and convenient and easy to use configuration features such as "whitelist by window" and autolearn. Can be used effectively without ever accessing the settings window. Tinywall is a rock solid non-invasive firewall that blocks everything by default with no notifications. This is an extremely secure interface unparalleled by the vast majority of other firewalls. The only security advantage a select few firewalls might have is if they come with HIPS protection. Other non-firewall software does have HIPS protection available, such as ESET NOD32 Anti-Virus.
Binisoft (freeware): Fewer features and more resource intensive than Tinywall (but still very lightweight). User friendly GUI that places all of the tools in one tabbed window. Notifications available for paid users.

Third Party Firewall:

I recommend using a Windows firewall controller, but if you would like to try something different, there are some alternatives. The following firewalls rely on active notifications which are popular because they impose finely grained control on the fly. They include a variety of bells and whistles that should, for the most part, be unnecessary if you are using effective anti-malware. They are worth looking into, but they are somewhat bloated, have been known to include PUPs in the installation process, and they may alter your web browser settings. I consider them to be obtrusive and heavy-handed, so I avoid them.

ZoneAlarm Free Firewall (freeware)
Comodo Firewall (freeware)

Anti-Malware

Malware is a general term which refers to viruses as well as other malicious software such as adware, spyware, ransomware, and bitcoin miners. It is important to use a strong anti-virus. It is also very useful to employ a specialized anti-malware program that stays up to date to protect you against a wide variety of rapidly evolving non-virus malware. Some anti-virus software is better than others at handling non-virus malware on its own. Some anti-virus programs (especially security suites) tend to be either invasive (ie. obtrusive: hinder specific tasks directly. it is not always obvious what is causing this burden, but in side by side testing you will find a big difference in specific tasks) or constantly use significant resources (ie. bloated: hinder everything indirectly), hurting system performance. Sometimes they are as bad as the malware they are meant to prevent. Low resource consumption should always be a key consideration here. Warning: all of these start at boot and run in background at all times.

Efficient Anti-Malware:

Webroot SecureAnywhere ($20*): I once had a list of many efficient anti-virus applications, but they have become more and more obtrusive and I have become disillusioned with anti-virus applications. There are many lightweight (not bloated) and effective options, such as Avast, but they are irritatingly obtrusive if you pay close attention and cause significant slowdowns. In my testing, Webroot Secure Anywhere (WSA) has been the only anti-virus application that has combined top of line anti-virus capabilities with an almost negligible impact on system performance (both unbloated and unobtrusive). While I highly recommend WSA, it is payware, so if you have a powerful computer I would recommend testing some of the more obtrusive free options to decide if it it's really worth paying $20 to avoid their burden.
Malwarebytes Anti-Malware ($0 - $25): Malwarebytes has no competition when it comes to protecting against non-virus malware such as adware, spyware, trojans, PUPs, bitcoin miners, etc. The free version is limited to only scans, while the paid version has active malware prevention tools. Because it is so specialized, it is a great addition to specialized anti-virus software.

Acceptable Anti-Malware

ESET NOD32 ($30/yr): Effective anti-virus with light to moderate resource usage. This is a relatively unobtrusive and lightweight anti-virus program, but it is not as streamlined as WSA. It is roughly as effective at anti-virus as any other paid anti-virus. HIPS protection works well together with TinyWall. Its HIPS protection might be slightly better than WSA's equivalent heuristics engine, and if so it would be the primary advantage NOD32 has over WSA.
Bitdefender Anti-Virus Plus ($60/yr): Performs similarly to NOD32 except that it has some additional features that might be either irritating or nice depending on how obtrusive an AV you're willing to live with. The interface is very modern but also convoluted and very disorganized. Bitdefender is often rated the number one anti-virus available, but this should always be taken with a grain of salt. It likely provides the best overall protection, but its improvements over NOD32 and WSA are marginal and they come at the cost of Bitdefender being somewhat obtrusive.
Microsoft Security Essentials (up to Windows 7) and Windows Defender (Windows 8 and beyond) (freeware): Windows Vista and 7 included antispyware called "Windows Defender" which was a mostly useless piece of software. The alternative was Microsoft Security Essentials which could be downloaded from Microsoft.com and installed, replacing Defender. It is far more effective anti-malware software. Confusingly, When Windows 8 came out, the original Windows Defender was abandoned and replaced by a new tool very similar to Microsoft Security Essentials, and this tool was also called "Windows Defender."

This is by far the least effective anti-virus solution on the list, but it is the only free option that I have found to be both unobtrusive and light on resource usage. If you want free anti-virus, you have to decide whether you want minimal systemic burden or effective anti-virus. MSE is much better than nothing, but it hardly competes with the other options. Be aware that the Windows Defender being described here is the Defender from Windows 8 and 10, not the Defender from Windows 7. In Windows 7, this software was called Microsoft Security Essentials, and it had a different "Windows Defender" which was actually a practically useless application.

Avast, AVG, and Bitdefender Free (freeware): These are all free options with strong anti-virus capabilities. They are much more effective than Microsoft Security Essentials, and they have very minimal idle resource usage, but they often interfere with common tasks and you will take a significant performance hit. In my experience, on computers that do not have powerful processors or low latency storage (eg. solid state), Avast is severely detrimental to performance despite its minimal RAM usage.

Inefficient Anti-Malware:

Any "Security Suite", "Total Security", or "Internet Security" package that goes above and beyond simple anti-virus is likely to be very bloated. It will bog down your computer and bug you with features that you don't need. The firewalls these come with are usually no better than using a Windows firewall controller. Go for as bare-bones an anti-virus as you can get. Get the anti-virus version and combine it with TinyWall and Malwarebytes; don't get a full security suite.
Norton, Kaspersky, McAfee, and ZoneAlarm: These receive very good marks as far as protection goes (similar to WSA, ESET NOD32, and Bitdefender), plus they are loaded with plenty of anti-stupid features to keep you from making dumb mistakes (similar to Bitdefender). Unlike WSA, ESET, and Bitdefender, they are very resource intensive and may frequently get in the way of normal PC usage. I recommend against these because they will most likely not do any better than WSA, ESET, or Bitdefender aside from irritating you more. The advantage of these applications is that they provide an wide variety of novel features that might enhance security if you use them correctly. Examples include the anti-keylogger and remote VM testing in ZoneAlarm. Unfortunately, many of these novel features have a potential to interfere with basic system usage as much as malware.

Using one of these is akin to choosing to live in a fascist dictatorship because you fear thieves, and this dictator murders all potential thieves immediately. The only thief you have to worry about now is the dictator, who is also a murderer. I have heard stories of ZoneAlarm randomly deciding to block basic Windows functions. Anti-virus programs are like system users who do everything with administrative rights and they do everything they can to avoid being tinkered with, so when they malfunction in this way it can be extremely frustrating. You should still apply the same "Security Suite" rule mentioned above. The only exception is that if you decide you want the bloat of ZoneAlarm, you might as well use its firewall, because ZoneAlarm does have a very good firewall. Otherwise, most of the distinctions between these four are superficial.

Cryptography

Encrypt sensitive documents to avoid identity theft. You should only use open source encryption protocols. Closed source encryption schemes are likely to contain back-doors, especially BitLocker, which I strongly recommend avoiding.

OpenSSL (open source): Beyond its use for asymmetric SSL encryption, the OpenSSL libraries are packaged with a command-line tool that can be used for on the fly symmetric encryption using a variety of algorithms.
AES Crypt (open source): AES-256, simple encryption of individual files into industry standard .aes files, context menu based. Very easy to use.
TrueCrypt 7.1 (not 7.2) (open source): A now defunct project that was in charge of perhaps the best encryption software available. This application is far from obsolete and is still an excellent encryption option. Full disk encryption, mountable virtual encrypted volumes (behave like a drive when mounted), variety of encryption and hash algorithms, hidden volumes (decrypts to one of two things depending on key used for plausible deniability). Wizards make this easy to use if you stick to default options. Available at truecrypt.ch, not truecrypt.org. Despite malicious rumors, TrueCrypt code has proven to compile to the distributed binary and has been audited and shown to lack intentional security weaknesses.
Veracrypt (open source): A fork of TrueCrypt with minor improvements to some of its technical weaknesses, developed by a private group. Interface is identical to TrueCrypt and now uses the same file format (did not in original version).
CipherShed: Community based open source project currently working on their first TrueCrypt fork release. CipherShed has teamed up with TCNext as a unified project. Ciphershed.org forums are dead, all discussion is at the TCNext website, truecrypt.ch.
GPG (open source): PGP based asymmetric key encryption. Asymmetric key encryption is used for secure communication. One key locks the door (this is your public key used by someone contacting you), but it cannot open the door. Only your private key can open the door. Give out your public key for others to talk to you, and use their public keys to talk to them. You use your private key to sign your encrypted message so others can verify it is you by testing it against your public key, but you never include your private key in the message―signing is a special task handled by GPG. Use key files (save keyring in a secure location) with public and private key information for secure communication. It seems strange at first, but it's easy once you get the hang of it. NEVER share your private key (or entire keyring) with anyone. GPG can also be used like OpenSSL for symmetric encryption.

VPN

A Virtual Private Network can boost your privacy by encrypting web traffic and keeping you anonymous over the web to combat identity thieves and other hackers. VPNs occasionally actually increase speeds due to bypassing WAN bottlenecks and ISP throttling.

AirVPN (Free or $60/year): By far the best VPN I have used with endless features, extremely high speeds (maxes out my 90 Mb/s speed without a problem), great customer service, and a wonderful and detailed interface. The free service has limited bandwidth so I recommend the paid service. You can forward up to 20 ports (I personally use 6, 20 is a lot!) and they even provide DDNS services. AirVPN is heavily focused around the security and privacy of their users.
Private Internet Access ($40/year): PIA is slower and less reliable with fewer features, poor IP sharing practices, unstable port forwarding, and almost nonexistent customer service, but they appear to be concerned with privacy and it is also one of the cheapest VPN services and provides a satisfactory service for most users.
OpenVPN (open source) + VPS ($0-$15/year): This takes a little command line configuration to start, but there are step by step instructions on the web. Setting up your own VPN gives you the highest possible degree of versatility. Ramnode offers 1 Gb/s, 500 GB/month (more bandwidth costs more), and a unique private IP address for $12 a year. To make an anonymous payment to Ramnode, use a pre-paid Visa purchased with cash registered with dummy credentials. There are many alternative VPS providers; Ramnode is just one of the most popular ones. Personally I use Crissic for my VPS and I am very satisfied with them; they are a great bang for your buck but also have a very strict AUP. There are also many companies that accept bitcoin payments for ultimate privacy. You can even use Amazon AWS for free, but they charge you if you go over your bandwidth limits, and they are not as concerned with protecting user privacy. Be aware that creating your own VPN involves a sacrifice in privacy because your IP can be more easily connected to your VPS than a privacy oriented VPN with shared IPs.

System Management

The following sections discuss software that can run in Windows which can be used in place of or alongside Microsoft Windows software in order to manage the system. These are unique from the aforementioned programs because they are not specialized to keep the system clean or stable. Rather, they are used for general system tasks that you probably already do all the time. These improve on fundamental system functionality.

File Management

File management tools do not necessarily improve the performance of the system (some do), but they improve upon the usability of core system tools, so they are worth mentioning.

File Manager

QTTabBar (open source): This is a great little dll extension to add tabbing to Windows Explorer. It's very simple, but there are a ton of options making it very customizable. This is perfect for someone who is fine with Explorer, but just wishes there was tabbing.
XYplorer ($30 for lifetime updates): Most features by far in a file manager. Dual pane (horizontal and vertical) and tabbed browsing also with an incredibly comprehensive tabbed details/search pane (also horizontal or vertical). The catalog is a great shortcut feature that goes beyond .ink files. The developer is great; I once contacted him about a feature I wanted and the same day he released a new version with precisely that feature. Optional custom highlighting which makes executables, video files, music files, text files, etc. all have their own font color, plus special files also are actually highlighted (eg. I have recently modified files highlighted green). You can also write scripts for your own custom features. XYplorer has proprietary tools for everything, and each one improves on what Windows has to offer. Often proprietary tools are irritating, but here they are all great. Great proprietary 32 bit context menu with "rename special" options that change groups of files' names according to certain rules. XYplorer does not support MTP. If you are a pirate who only pays for things very rarely out of charity when they are truly phenomenal, consider paying this man. He has single-handedly created what is in my opinion the best file manager in existence. I say this as an Arch Linux user who has used dozens of file managers.
Directory Opus ($50 - $90 for only current version): This is a very nice alternative to XYplorer. It doesn't have quite as many features, but it is 64-bit. Rather than develop their own proprietary tools for everything, they rely a bit more on Windows features that already exist, so it recognizes MTP and uses the normal Windows 64-bit context menu. One proprietary thing that DOpus does have is its own file copier, but it isn't as good as some other third party copiers. While XYplorer has a very ergonomic and utilitarian interface, and both have very modern features, DOpus has a more attractive and modern aesthetic, and toolbars can be moved around a bit more freely.
xplorer2 (free or $30 for pro version): This is a great alternative to Windows Explorer + QTTabBar, but it is somewhat outdated and lacking in features compared to DOpus and XYplorer. The one advantage it has over those two is that pane placement is much more custom. Anything can go anywhere, and anything can turn into a menu style item (eg. click to bring out the tree as a temporary overlay on the left or right until you click elsewhere). If your only concern is a customizable interface, xplorer2 might be for you.

File Copier

Improve performance and reliability over Windows copier.

TeraCopy (freeware): The most feature packed with above average speed and reliability. Pause and resume copies, verify results, and directly monitor and control which files are being transferred as the transfer is taking place.
FastCopy (open source): The fastest. No special features.
Unstoppable Copier (freeware): The most reliable with decent features but very slow. Data recovery and corrupted file transfer.

File Indexer

Everything (freeware): This indexer works far better than Windows Search. Its service is far less intrusive; it doesn't eat up CPU cycles like the Windows indexer. Also, search results are shockingly instantaneous even on a PC with several drives and millions of files. Make sure to disable Windows Search in Services.msc if you choose to use Everything.
Copernic Desktop Search (freeware): This indexer not only indexes file names, but the textual content of all files. This is very impressive when done well but it is almost impossible to avoid a high burden on system resources. I have not yet tested this application because I assume it is not worth the systemic burden for my purposes, but I have heard good things about it.

Download Manager

Like file copiers with your OS, these improve the performance of web browser downloaders and give you plenty of features. Never lose another partial download again. There are many legal uses for torrents. The torrent protocol reduces server load and permits extremely high download speeds for well seeded torrents. For example, Linux distros and Android ROMs are best downloaded via torrents.

Download Ninja (freeware): An excellent new feature packed download manager with a simple and intuitive interface. Very active development. Runs in background by default. Make sure to get the appropriate add-on or extension for your preferred web browser.
Free Download Manager (open source): A more traditional download manager with a layout similar to Deluge and μTorrent. Very nice and versatile application that can handle both http and torrent downloads.
Deluge (open source): Rock solid torrent software with similar interface to μTorrent. It is primarily designed for Linux but works great in Windows also. It has many plugins making it more feature rich and extensible than μTorrent. It comes with built in torrent organization by tracker which is a great feature.
Transmission (open source): Nice alternative to Deluge that works great but it is also much simpler with fewer features. I prefer Deluge.
μTorrent (malware): Avoid this application at all costs. μTorrent was once a great application before it was bought out by Bittorrent Inc. μTorrent is now very bloated software that is packaged with adware and occasionally other types of malware such as bitcoin miners. It is harmful for your computer and should be treated as malware.

Shell Customization

These directly add to, modify, or replace fundamental system elements. Some of these provide functionality to Windows that is typically only found in Unix-like systems.

AutoHotkey

I wasn't sure where to put this as it is extremely versatile. Autohotkey was one of my most used applications in Windows before I transitioned to exclusively using Linux. It gives you the ability to very easily write programs to customize specific Windows features far beyond the capabilities built into Windows. The potential is limitless. It is a truly great tool that supplements Windows' relatively weak batch scripting. In conjunction, they rival shell scripting in Unix-like systems.

Autohotkey is by far the most difficult application to use on this page, as it requires you learn a unique language if you want to create your own personalization. However, it is extremely easy compared to lower-level languages such as C or C++ (even C# is relatively low-level in comparison), plus there is a huge selection of complete .ahk files already written for specific tasks that can be found online in various forums and websites. You do not have to learn the language to use these files, but they can only be customized via text editing.

AutoHotkey is derived from an old version of AutoIt. AutoIt at the time was very limited, but today it has become a very powerful language. I have not used it, but while remaining a very high-level language, it appears to operate at a slightly lower-level than AutoHotkey with greater capabilities and a steeper learning curve. One of the huge benefits of Autohotkey is the speed and simplicity of deployment for tasks that would be rather complex to code in more versatile low-level languages. AutoIt seems to be a compromise between the two.

Desktop Managers

These work with the existing Windows shell (explorer.exe) to provide additional features.

Switcher: This provides the wonderful OS X feature, Mission Control, to Windows. It displays all of your open windows in such a way that you can see the entirety of every window. It is a huge improvement over the alt+tab and win+tab functionality in Windows. It was designed for Vista but also works in newer versions of Windows.
Dexpot: This is easily the best and most feature packed virtual desktop manager for Windows (far superior to VirtuaWin). With this you get the functionality normally only seen in Linux of having as many desktops as you want. You can also add the same widget to your taskbar displaying a mini version of each desktop which you can click on. There are a huge number of features (including what Switcher does) and you can use any keyboard or mouse hotkey/shortcut to get to them.
Windows 10: The above features have finally been included in Windows 10. They are much simpler and far less configurable, but their native presence deems the above unnecessary except for those with the most discriminating taste.

Shell Replacements (CLI)

These provide as little as a command line interface or as much potential as allowing entire other environments run alongside Windows.

PowerShell: PowerShell is a much more advanced alternative to Command Prompt designed by Microsoft with capabilities closer to a Unix-like shell. I highly recommend using this instead of cmd.exe for advanced users. Be aware that PowerShell does not have full compatibility with CMD/batch. However, when batch files are run in PowerShell, they are interpreted by cmd.exe. In Windows 10, there is a built in package management system similar to those found in Linux systems.
Cygwin: Cygwin is a third party collection of tools which provide Unix-like functionality within a somewhat isolated environment inside Microsoft Windows. It can be used to control Windows applications and files while also operating its own subsystem. The foundation of Cygwin provides a Unix-like directory structure and a Unix-like command line. It's repositories include many GNU applications typically found in GNU/Linux and FreeBSD. I highly recommend Cygwin for users familiar with Unix-like systems (which includes OS X).
MinGW: Minimalist GNU for Windows integrates basic GNU tools directly into Windows. It is much more integrated than Cygwin as it does not require its own pseudo-environment and set of libraries. MinGW binaries can run directly in command prompt. At the same time it has a very minimal selection of fundamental GNU tools, whereas Cygwin creates a whole Unix-like environment, going so far as giving you the capability of running a full Xorg based graphical interface with a desktop environment.
Interix: Interix (aka Subsystem for Unix-based Applications or SUA) is a POSIX-compliant Unix subsystem developed by Microsoft to work within Windows. Unlike Cygwin, which lives on top of Windows, Interix exists at a lower level and interfaces more directly with the kernel, providing an experience that is more like a native operating system shell. Also unlike Cygwin, it has far less development and attention. Development ceased after Windows 8 and it is no longer included in the system.

Shell Replacements (GUI)

These replace explorer.exe as the Windows Shell. This means that you no longer have the Windows taskbar, so they have their own modules which can be combined together to create a very customized interface. These seem to have been declining in popularity as development has stagnated on many of these, but they are all still available. The biggest problem with these is that they all abandon the Windows start menu. One should be able to replace the taskbar without losing any ability to use the start menu. Some so called "shell replacements" simply change the appearance of the Windows shell, so they have not been included.

Sharpenviro (discontinued): This is perhaps the most complete and easily configured of the Windows Shell replacements. It has many features and resembles GNOME. It uses toolbars (like a taskbar) with widgets on them.
Emerge Desktop (development stalled): This is one of the most popular replacements and works differently than Sharpenviro. It uses modules that are like chunks of a taskbar. They can be moved around anywhere on the screen, making the appearance very customizable, but there are not many features.
LiteStep (slow but active development, check out alpha builds here): This combines the module concept with a huge amount of features. There are countless user developed modules available in the LiteStep community.
KDE Plasma Desktop (development stalled): KDE for Windows works great, and KDE Plasma Desktop a superb (albeit quite heavy) desktop environment. Unfortunately, plasma-desktop.exe is the only part of KDE that has not transitioned well to Windows, because it is designed as a front-end to the X Windows System. Likewise, it would require a rewrite to really work seamlessly with Windows. Some people have had success using it in Windows, while most people have only been able to create one toolbar where the only thing that works is the start button (displaying only KDE applications). Another thing to consider is that the Plasma Desktop can only support KDE applications. You can open normal Windows applications using explorer or another file manager, but the KDE launcher and task manager will only show KDE applications. So this is not yet a good replacement for the Windows shell, but it can be used in conjunction.
XWin: This is a port of the X Window System to run over Cygwin. Like KDE, it is not a full replacement for Windows Explorer. It can run in windowed mode. In this situation you need a window manager and can run a full desktop environment such as XFCE, LXDE, KDE, or GNOME (which include window managers) encapsulated within a Microsoft Windows window. Windowed mode in fullscreen would be practically indistinguishable from a Linux environment, except that it runs on top of Cygwin and the Windows kernel and likewise relies on Cygwin's package manger. You can also run XWin in multiwindow mode which seamlessly integrates XWin windows into the Windows desktop. Unlike windowed mode, in multiwindow mode you must use the Windows taskbar.
Gentoo Prefix for Interix: This is an entire Gentoo Linux system which runs over the Unix-like Interix.