Since I mostly go to a club for the actual music I tend to prefer the Zoo at l'Usine or Witamix, since that's where they tend to get jungle/trance/glitch DJs. Of course your milage may vary.

If you have other motives you might like, say, Shaker's as it seems to be the dive of choice for young expats, or at least it was when it was in the old town. I could never stand the music, but I've seen people have fun there. Also of note is the Ahambar which is upstairs from the Alhambra theatre in the old town. It's more of a lounge, but they have interesting music, and are very much favored by the Au-Pair set.