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A short answer is WP:NOTDIRECTORY.

Hmm... what about
I don't want to waste neither your nor my time arguing, I am new to editing Wikipedia, but
I don't see much (any) difference in linking directly to external site (until the appropriate wiki page with the software description is created) vs. a wikilink to a description of that program (or you would consider creating such page as an advertisement and will also block it???).
I can definitely agree to Wiki is not a A complete exposition of all possible details, Wikipedia is not a manual, guidebook, textbook, or scientific journal
And I think, this is exactly why many wiki pages have 'External links' (in contrast to References that support what is written on the wiki page itself) - to provide a link to a place where a more technical relevant information can be found. Link to an external software page (especially if it has a technical description of how TEM works and how simulations of TEM are done) is exactly this kind of info.

Another is WP:UNDUE - you are selecting one out of many; There are so many TEM simulation codes that their mere listing would overflow a page.

Well, I wouldn't argue if that was the case. But when I needed one (same for Bader analysis), I spent A LOT of time to find at least one. So I just wanted to help others by providing a link to it in a place where people could really find it.

further, 99.9999% wikipedia readers would never even think about simulating a TEM image.

I agree, but those readers would not ever think of visiting TEM page in the first place. I believe that pages on more or less technical questions are read by people who are potentially going to use this technology, and thus might be interested in even more technical information. See my comment about External links above.

Those links might be appropriate in a dedicated article (say on TEM image simulation), and you are welcome to write such an article (or even better on STEM; I know I won't have time for that) but not in the TEM article itself.

That's exactly the point - I am not going to write such a page, neither the author of such software.
Letting people to add such external links (given that they are indeed relevant) quasi-temporarily seems as an appropriate solution to me. As soon as you will see that there are too many of them, an editor would have a good starting point to start a new wiki page with a comparison table or with a description of each software. If you block such edits on the other hand you artificially create a barrier to add new potentially useful content to Wikipedia.

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This might help:

  • Wikipedia (WP) is a constant work in progress - many articles need a basic cleanup.
  • Wikipedia encourages links to its articles, but not to external sites, unless those links are essential to verify WP information. The reason and the difference are simple - external sites are volatile, and are beyond WP control.
  • Partly for the above reasons, "External links" section can be trimmed or blanked any time and this happens quite often. Again, wikipedia is not designed to serve as a collection of links. The argument "this is too technical, so lets link to a page where this is explained" doesn't work - links are too many, and we can't evaluate them.
  • Page views, FYI, [1] [2] - this is rather high for a technical topic. Cf. [3] (technical topic).
  • TEM codes are many, they just target very narrow categories and thus are not advertised.
  • Any information is useful to someone. However, wikipedia can't be stuffed and must be selective. The selection is soft and is based on policies and consensus (among wikipedia community) - it is not that I myself (or any other editor) have decided "this shouldn't be there". Materialscientist (talk) 04:16, 16 February 2011 (UTC)[reply]

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  • Thanks a lot for the stats page. BTW STEM http://stats.grok.se/en/201101/Scanning_transmission_electron_microscopy seems to be much more technical.
  • I still disagree that creating an article about some software (which inevitably would have an external link to that software, and the article existence makes sense only as long as the software exists) is any different from a direct external link.
    It is quite acceptable to create wikipedia (WP) pages on a specific program, if it is notable. Usually a page is created on simulation software, to separate specifics from basic explanation of the topic itself. Materialscientist (talk) 23:40, 16 February 2011 (UTC)[reply]
  • Similarly, I disagree to links are too many, and we can't evaluate them. This is exactly why wiki works well - there are MANY editors, the editors CARE about their content i.e. THEY chose what to write (i.e. those ARE evaluated links) and monitor their pages constantly.
    This is a common misconception. There are only a few thousands of active editors and millions of articles. Manpower is lacking everywhere, especially in science topics. "Can't" means not only we don't have time - wikipedia is also not meant to rank sources (though often it has to). Volatility of external sites is also an issue. Materialscientist (talk) 23:40, 16 February 2011 (UTC)[reply]
  • So what do you suggest to do with CTF Explorer external link on HRTEM? Or would you agree to add one link to QSTEM on the STEM wiki page? Need to be consistent...
  • Thank you for explanations, it would take me ages to find out about all that wiki policies by myself.
    Don't hesitate to ask. WP "rules" often look scary and mysterious at first sight, while they are very simple and logical. Materialscientist (talk) 23:40, 16 February 2011 (UTC)[reply]