These are all very solid resources for learning Japanese, from my experience.
smart.fm = Well organized kana and vocab flash cards (in Flash! lol). Also quizzes you during these flash card sessions. I like this site, because they show you kanji with the vocab and have audio samples.
lang-8.com = Language exchange social networking. Write random (or non-random) journals in Japanese (or whatever foreign language you want) and have it corrected by others.
guidetojapanese.org = Amazing resource of Japanese grammar.
jisho.org = Online Japanese dictionary.
alc.co.jp = It's in Japanese, but don't let it scare ya. If you type in English words, it not only translates them for you (no romaji, though ^^; ), but also gives TONS of example sentences about those words in BOTH languages.
Japanese.about.com and kanjisite.com get honorable mentions, because although they're not as robust as the above sites (IMO), they're quick and easy references for anything related to Japanese and kanji.