FWIW, I think I've used all the flashcards programs there are and none of them do what I would like.
Right now, for vocabulary I use wakan, and it is an awesome program. BUT...
I wish the examples were better integrated. (For instance, the example sentence, with the example word itself replaced by a dash, could be available as a prompt.)
I wish users could easily add their own examples. Usually I encounter words and phrases in context, so I could just enter part or all of the sentence I found it in. This is especially important with phrases, because the wakan example database doesn't have examples for phrases.
Since I try to learn the associated particles with the vocabulary word, I wish there was an easier way to display this information. Right now I stick the particles in the "phonetic" field. So, to take an example, I have two cards for the word 大事. On one card, the meaning field is "(to be) a big deal" and the phonetic field is "おおごと(だ)" -- except wakan won't allow parens in the phonetic field.

For the second 大事 card, the meaning field is "important" and the phonetic field is だいじ(な). Similarly, if a verb takes に or を or と, I note that in the phonetic field.
I wish that the "meaning" field could be entered in Japanese if desired. I am trying to use the Japanese-English dictionary less and less, and this would be a step in that direction.
Oh, and I wish there was a Leitner-like box system. Right now I just let wakan give me 25 or so random words, drill 'em till I know 'em, and throw that list away. Over time it works, if I adjust the value for testing new vs. known words... but a box system would make me confident that fewer words were falling through the cracks.
Anway, I don't mean to speak ill of the program. It is a very nice tool, and free to boot. I would hate to do without it. Kudos to the author!
P.S., while we're on the subject, does anyone know a kanji flashcard program where you can request to be quizzed on all kanji with a given ON reading? I have been making lists like this in Lexikan, but it is time consuming.
Shira
"Give me a fruitful error any time, full of seeds, bursting with its own corrections. You can keep your sterile truth for yourself." -- Vilfredo Pareto