Circus, the Tokyo offshoot of an Osaka club, is aggressively underground: small, out of the way, in a basement (of course), with no decor to speak of and all attention laser-focused on the often experimental music. It's open most Fridays and Saturdays from 11pm, and sometimes other nights; check the schedule online. Cover is ¥2000 to ¥3000 and drinks ¥600; ID required.
Wear your comfy shoes because there's nowhere to sit.