Muse has a great mixed crowd of Japanese and foreign office workers. It's a large club that plays pop.
Ageha has a primarily older, well dressed Japanese crowd.
A large space for events. Check the schedule.
8. Club AirAir appeared in the movie Lost in Translation.
5. Club Asiahttp://www.clubasia.co.jp/
A Tokyo classic that's been around forever and a day. They still pull in large crowds on weekends.
6. HeartlandHeartland is a lounge just outside Roppongi Hills. It's popular with investment bankers and people who want to meet investment bankers.
Womb is one of the largest nightclubs in Tokyo (and the World). Bring your id.
8. Le Baron de Parishttp://lebaron.jp
A club with some interesting events. Check the schedule.
9. La Fabriquehttp://www.lafabrique.jp/
Loads of events hipsters might like.
10. Gaspanic TokyoA popular chain of clubs in Roppongi and Shibuya. They sometimes get weird about id if they think your skin is too brown.