Some of the web sites I have collected and used while living in Japan for a year or so. Please leave any suggestion in the comments below and I'll add and update from time to time.
Get Hiroshima: A comprehensive Englisg guide to the city of Hiroshima.
Japan Visitor: For travel accommodation & culture.
Kansai scene: One of Japan's biggest bilingual magazines.
Outdoor Japan: For outdoor adventures in Japan.
Quirky Japan: For all the weird and wonderful that japan can offer.
35 Degrees: Entertaining stories about making friends as a foreigner in Tokyo.
Snow Japan: For those who love winter sports.
The Gaijin Pot: For foreigners trying to make it in Japan.
JapanesePod101: Learn Japanese on your iPod.
World Nomads - Japanese for your iPod: World Nomads Language Guide - Japan.