Dictionaries

Jeffrey's Japanese <_> English Dictionary — A very useful site.
US mirror, US mirror 2, or US mirror 3
Australian mirror
Jim Breen's WWWJDIC — Need to make your own dictionary?

Learning Japanese

Joyo 96 — A great site for learning resources.
Pera Pera Penguin's 5 minute Japanese Class by Hitomi Hirayama — Requires Acrobat with Japanese fonts, but worth it.
Japanese Public Broadcasting — Also in English
japanese.about.com — Many topics covered here.
Charles Kelly's Web-based Japanese Language Study Materials — Handy quizes and lessons for Kana and Kanji.

Bookstores

Kinokuniya — Sites on the East and West coasts and throughout Asia.
Sasuga Books — A good selections of books and no international shipping.
Amazon Japan — Everything you want, but international shipping charges apply.

Other

Google Japanese — Need I say more?
Google's Japanese Web Directory.
Yahoo! Japan — Searching for something in Japanese is a lot easier when you know where to look.
Yahoo! Directory: Japanese