DreamKana is a freeware hiragana and katakana flash card application. It is easy to use and flexible to the way you want to learn. It includes voiced constanants in both kana sets, and does not require any special fonts or language packs.
LingoLessons is flashcard-based software that helps you learn foreign languages easily. It is unique in that it operates in an entirely discreet fashion. It runs in the background on your computer and asks you questions at set intervals. It is designed to be suitable for both office and home use. Includes Japanese katakana, hiragana, kanji and vocabulary lessons.