I wouldn't say Bodega is a good venue - there's giant pillars in the way
I've always enjoyed James Cabaret and San Fran gigs.
Haven't been to James Cabaret since it's been James Cabaret but saw the Black Keys there about 7 years ago when it was the Front Room, and it was an awesome venue then (and a great gig)
Edit: Well, I went into James Cabaret last weekend for the Greek food festival but I don't think that counts