Popular Sites on Japan

Here is a list of my recommendation of sites on Japan.
JapanReference is probably the most extensive listing of sites relate to Japan. If you are looking for something specific, go there first.
Metropolis is a general site with a visitor guide, restaurant and cinema reviews, news (Japan Today), housing, job search  and classified ads.
In the media section, I recommend  the
Yomiuri Online, News on Japan and the Mainichi Daily News for its tabloid "wai-wai" stories. You can also listen to Radio Japan (NHK) in no less than 22 languages.
If you live in Japan and are interesing in talking about your experiences, read other's and meet people, you should try
Japan.box.sk, Fucked Gaijin and the Young Dudes Guide to Japan.
If you are travelling, check first the JNTO's site (available in 8 languages). Others useful and interesting sites are listed by categories here.
News
General
Cool
Tourism