This page will eventually include links to both flashcard software and collections of flashcards.
You'll want to use a flashcard program supporting a spaced repetition method such as the Leitner system, which is a very efficient method of learning vocabulary and Kanji.
- Anki is very good, and is the one I would recommend everyone try first. Nice interface, effective scheduling, very customizable, many pre-built decks available, can synchonize decks between multiple computers and even allows you to access them on the web. You'll have to read the instructions in order to understand all that it can do for you.
- Mnemosyne seems to be popular. I have not used it since Anki currently suits my needs.
- I've used the simpler Jmemorize in the past, though it hasn't been updated in a while. Try Anki first.
Apparently there are also websites where you can edit, store, and practice with flashcards. I'll look into those too at some point.