Statistics and Other Additional Features
Although as part of the research project Mnemosyne tracks several statistics, only the simple stats are available directly in the graphical interface. Basically, you can see how many cards are in your collection, what percent of the cards have which grades, and you can see a calendar for the next week of how many repetitions have been scheduled. There are also individual card statics but I don't think that level of information is very helpful by itself when learning. However, even though Mnemosyne doesn't offer much information, and a new statistics package is in development, I don't really feel any need for it myself. Of course, I judge my learning by how well I'm able to read books, and I'm not so easily charmed by statistics. If they are your thing, Mnemosyne is a real disappointment-- moreso considering it's collecting that information for research, just not making it available to the user.
Anki has far more complete statistics support available within the interface, including some nice graphs. Some of the extra information is useful and some of it isn't. However, I don't like the interface for changing the interval of the graphs, as you have to use the scrollbar as a button, which confuses the metaphor of the scrollbar.
SuperMemo, however, is the statistics king, not only because it offers comprehensive, totally configurable reports on everything, but it also helps you easily find the cards you miss most often so that you can review them, split them up, and make them easier to remember. If you love stats on everything, this is the program for you. Of course, like most of the rest of the experience with SuperMemo, you have to put up with a pretty awful interface to do this.
Anki has a few really great time-saving features for making cards. (Note: both Anki and Mnemosyne have many pre-made decks available for download. I do not recommend using any of the prebuilt decks, because much of the value of spaced repetition software comes from building your own deck. If the thought of building your own deck seems like too much trouble, you're probably not going to do your repetitions every day, and you'll probably stop using spaced repetition software entirely within a few months.)
One is that you can automatically type in, say, a question and have furigana for the kanji inserted into the answer. The system isn't perfect (my guess is it's using Jim Breen's dictionary), but it's accurate so often that I only needed to make one or two edits to about 20 cards out of 500-- a real time saver.
Another, perhaps even bigger time saver is that Anki allows you to enter several pieces of information (kanji, reading, meaning, etc.) and then make any number of cards based on those facts. While the interface for this and terminology could use some polish, once you figure out how to use it you can save a lot of time since you don't need to reenter any duplicate data (sometimes this is necessary in Mnemosyne).
The only thing to remember is that if you're using this feature (or Mnemosyne's "add vice versa" feature), never go from English to Japanese (unless you need just a few expressions). If you're trying to attain fluency, it's much harder to get the nuances of the words if you do it by remembering the English equivalent. The reason for this is that many words have several senses in both languages, and most of them don't map to each other. Also, make sure you don't add cards you don't actually need to remember. In Anki, this means that with the default settings, you have to either enter your definitions in Japanese (without English, since if you have both you'll just read the English) or turn off the creation of the "Production" card (which is on by default.
SuperMemo's incremental reading is the only feature of its kind. It might be worth it to purchase the software (and still use Mnemosyne or Anki instead) for that reason alone. However, until you can read Japanese without too much trouble (and without Rikaichan) it won't help you much, so I will just note it here and move on.