You got Womb, Unit, Module for harder stuff in Shibuya and Harlem for hip-hop/r n b. A visit to Yellow is well worth it, just for the soundsystem.
Plenty of concrete holes/small clubs like Milk, Fai Aoyama, Mixrooffice, No style etc with good music and friendly staff.
For Kobe/Kansai check out http://www.kansaiscene.com/2006_03/html/club.shtml