Some general Japan and news links that may be of interest.
Japan News Sites
The Japan Times
The New York Times – Japan
The Asahi Shimbun / IHT
Asia Times – Japan
The Daily Yomiuri
Hyperdia – Train timetable information in Japan (searchable in English).
WikiTravel – A free and editable travel guide. Good for major destinations.
Explore the Heart of Japan – A good guide for the Japan Alps (Niigata & Nagano)
Jorudan – Train Route Finder (English)
Japan Bus Web – information on using the highway buses in Japan
etour.co.jp – discount air tickets etc.
No.1 Travel – discount air fares
STA Travel – discount airfare, affiliated with the student travel service by the same name in the United States. Most discounts do not require student status.
JET photography on Flickr (more than 1200 photos and nearly 100 members)