Japanese Pod 101--great Japanese podcasts and other programs for learning! Possible to get some for free, but the great majority of programming comes with a price.
Smart.fm--many great quizzes and games to study Japanese and other topics for free. Premium subscriptions also avaliable
Lang-8--wonderful tool in which you can study your target language through journaling
Skritter--nifty way to practice and learn kanji (if a bit pricey)
Reviewing the Kanji--good way to review kanji in conjunction with James Heisig's Reviewing the Kanji book.
Shared Talk--great way to meet other learners and practice language in both voice and text chat. Free!