Learning Japanese
Tae Kim's Japanese GrammerThis site covers about the first two years of college-level Japanese grammar.
JWPce Japanese Word Processor
The best Japanese word processor I've found so far, easy to use and doesn't require an IME. A Japanese/English dictionary is included, just press ctrl+d while in the program.
Jim Breen's WWWJDIC Japanese Dictionary Site
Some people swear by this site, I prefer the one included with JWPce.
Space ALC
A good site to look up how a given Japanese word is used.
About Japan/Current Events
Japan FocusDeals with issues like global diplomacy, World War II, racism, and Japanese culture. Not exactly light reading, but interesting none the less.
The Asahi Shimbun
The 2nd most read newspaper in Japan translated into English.