There are heaps and heaps of online Japanese study sites out there. A quick Google search will find many. The following sites have free materials, and come recommended by ALTs.
Sabotenwebfs huge collection of Japanese language sites on the web (some links broken):
The Japanese Page
Grammar, vocab, JLPT resources, kanji-a-day emails.
Meguro Language Center
A great website with lots of free grammar, vocabulary, and JLPT resources.
Pera Pera Penguin
Conversation lesson column from the Daily Yomiuri, downloadable for free.
Good story-based lessons. Can provide online webcam lessons with a tutor.
Nihongo o Narau
Very good overall study sight. Continually being expanded.
Nagoya University Grammar Drills
Grammar and expression collection
Cornell University Language Center Listening Links
University of Victoria, British Columbia Listening Exercises
Stanford University Listening Exercises
Yomiuri News Stream (for Windows Media Player and Real Player)
Vocabulary resource with voice commentary. Scroll over the words/pictures to hear the correct pronunciation. Also has kana writing practice.
Make your own online word lists, flash cards and written tests.
Kanji, Kana and Reading
Teach yourself Japanese
A handy site with excellent explanations and sound files to help pronunciation. Main focus is kana and vocabulary, though also has grammar explanations.
A great site for studying kanji, especially if you aim to take the JLPT. Includes level 3 and 4 kanji tests and preparation.
Study resources, including tests and sound files.
Kanji a Day
Daily kanji, listings, JLPT information, etc. If you register, it will remember your level, and choose appropriate kanji for you.
Online Java Kanji Game
Interposes itself between your browser and the text, gives you the reading and meaning of kanji when you move your mouse over them.
Collection of out-of-copyright Japanese literature.
A web-based pop-up dictionary: move your mouse over a kanji online and the translation will appear.
The Japanese Slang Jisho
Great site for learning common Japanese slang.
Banbutsu Dai-Jiten Encyclopedia
Move your mouse over the links on the left for English category names):
A website for JETs, the first page features downloadable language study software, including kana and kanji programs. The second page includes software downloads that enable your computer to read and type Japanese fonts.