Japanese Cities

Japan 101
http://www.japan-101.com/

Japan-guide (and many ads)
http://www.japan-guide.com/list/e1000.html

Japan Knowledge [This site can be accessed only from school]
http://na.jkn21.com/

Japan National Tourist Organization
http://www.jnto.go.jp/eng/index.html

NationMaster Encyclopedia – list of cities in Japan
http://www.nationmaster.com/encyclopedia/List-of-cities-in-Japan

Regions and cities of Japan
http://web-japan.org/region/