General information
japan-guide.com: This site provides very wide range of information.
Japan Student Services Organization: This site provides general guide for international students in English, Chinese, Espanol, and so on.
International students offices of universities
Major national universities offers information which are worth visiting to students in other universities.
University of Tokyo: This site offers not only for general guide for students but also some information on exchange programs and scholarships awarded by government/non-government organizations.
Tokyo Institute of Technology: This site provides general guide for post-docs. Also, they have job listing in the institute. (But, you should know this institute is one of the prestigious universities in Japan. Competition is very tough!!)
International Student Center, Osaka University: They provides detailed information for international students. If you look for information on living in Osaka or Kansai area (central part of Japan), this site is must-see website.
KUFSA, Kyushu University: Information on living in Fukuoka and Kyushu area (west side of Japan) is available.