Although far less popular than J-pop, J-rock, or Electronica, ska music has a definite presence in Japan. Emerging about a decade ago with forerunner bands Ska-Flames and Tokyo Ska Paradise Orchestra, the Japanese ska scene saw a huge popular surge in 1997 (mirroring the burst of popularity in the Unitd States) which quickly died out. However, many Japanese ska bands continue to persist despite a lack of mainstream support. The Determinations, The Side Burns, and Blue Beat Players are Japanase ska bands popular among fans of the genre.
Skanime Nation: Website which provides information and links on Japanese ska music.
The Japanese Ska Page: Small, simple page with links to a large selection of Japanese ska bands.
Another less-mainstream genre, Japanese punk, has a significant underground following (as does punk music in the United States). The punk scene has existed in Japan about as long as it has in the U.S., dating back to the late 1970's. And just as it has in the U.S. and Europe, the punk scene has gone through various reincarnations with different styles and tones emerging, disappearing, and re-emerging.
The Japan Punk Project Home: Great site with tons of useful information on Japanese Punk.
In Dog We Trust: Website with tons of photographs of Japanese punk/hardcore bands.
J-Underground: Site with lots of information on Japanese punk and hardcore bands.