The Japan Window is a project at Stanford University, and has many great links to Japan. Too bad it has gone down until further notice.
When traveling to Japan, be sure to check out Japan National Tourist Orginization.
Global Window - Japan (req. Frames) is very fancy, new and framed. It is mostly intended for business people, and is produced by UCLA, Meikai University and Asahi University.
From the University of Washington, a great page from the Technical Japanese Program. Down in Australia, Monash University has a big FTP archive with lots of Japanese links. Also in Australia, the folks at Lavasoft have some interesting Japanese products for sale.
If you need to read web pages in Japanese, you can try Shodouka, which will display kana and kanji. This is such a nice service, and it's free, so don't be suprised if it is busy. Keep trying!
They're big. They don't wear much clothes. They've been around for a thousand years... now you can visit the offical Japanese Sumo web site!
Japanese comic books (manga) and animation (anime) have a very fast site on the web: EX. Another similar fad in Japan is the Virtual Idol, such as Kyoto Date. Also, be sure to check out Otaku World for lots of Manga and Anime.
If you're hungry, and riding the train system in Japan, why not pick up an Ekiben Obento? They're delicious! For info all about Sushi, visit The Sushi Guide.
There is a new museum in Tokyo, with exhibits which blends photography, film, video, and computers. The Intercommunication Center (ICC) seeks to conceptualize a prosperous future society by promoting a dialogue between art and scientific technology.
A map of the prefectures can be found at here. For a trip to the past, visit the Edo Period site.
Sometimes, famous American movie stars are used to sell products in Japan. Here is a list of celebrities who have sold out.
Here is a Japanese-English Dictionary.