Stability, Documentation, and Support
Mnemosyne has been in development longer than Anki and is better tested. The program is stable. It does currently have one horrible flaw, which is that if the OS crashes (Windows, Linux, Mac OS X) while you're working on the program, you will lose many of your repetitions since your last save (or the last time you opened the program). This isn't much of an issue on Linux and OS X, but my Windows machine crashes fairly often, and this has occasionally been a source of frustration.
Anki, on the other hand, is in rapid development and it sometimes shows. I noticed that the countdown to next repetitions periodically displayed negative minutes, for example. However, the worst bug I encountered was that it repeatedly showed me certain cards, even though I continued to mark them with the highest possible grade. I am informed this error has since been fixed. On the other hand, this was an error in an official, not a beta release of the program.
In fact, when I originally wrote this review, I was more likely to forgive Anki of its bugs since I thought it had only been in development for six months. Now that I am informed that at that point Anki had been in development for about a year and a half, I am more disappointed to see so many bugs. But, at least Anki has a very functional autosave feature.
By far the worst, though, is SuperMemo. Part of this is that SuperMemo is deeply tied to Internet Explorer for learning Japanese, because it supports Unicode by way of HTML. Since Internet Explorer is full of bugs, it only makes sense that SuperMemo is as well. However, SuperMemo also has more than its fair share of its own bugs, despite being more than twenty years old. In six months of using SuperMemo, I had to restore from a full backup three times, each time losing six to eight hours of work.
Mnemosyne is fully documented. Disclaimer: I have contributed to and now edit the documentation for the Mnemosyne project.
Anki has a wiki but many of the pages have no content, including (currently) the page for "adding cards." Although one may not need documentation for such a simple feature, one would assume such a page would cover advanced features about adding cards, or not exist at all.
However, Anki does have five screencasts (where you can watch a short video that introduces the program), which serve as a decent introduction to the program. However, I prefer to have a manual that I can print if necessary.
SuperMemo has an excellent website full of extremely helpful articles-- but scattered about in a haphazard fashion, many of which have not been updated for years (and reference old versions of SuperMemo). Still, the place is a goldmine, and I would recommend all users of any variety of spaced repetition software take a good look at the site and its many articles, most of which concern the seemingly simple but in fact very tricky process of making "easy to remember" flashcards.
In particular, I recommend 20 Rules of Formulating Knowledge.
Both Mnemosyne and Anki have active forums where you can get help quickly. The developers of both Mnemosyne and Anki are very active on their respective forums and always ready to help when they can. Here, you can't go wrong either way with open source.
SuperMemo, on the other hand, has a mailing list and a wiki, both staffed by users. Now, the users are fairly helpful, but since you paid a company for the software, you might expect good support-- but you won't get it. If you have a problem with your downloading or activating the SuperMemo software (it's not terribly simple), than you can get decent (though not great) support for that. But if you need any help using the software, expect to be referred to the (not very well organized) website, if you even receive a response at all.