Vanilla Mood is a cool little jazz bar/club just across from Roppongi Hills. It has been open for sixteen years, run for the last five by Amagai Ken-san.
Amagai-san hosts events there almost every evening, ranging from DJ nights to improv sessions to straight-ahead swing. He's putting a lot of effort into making the space one that is both casual for customers, but also serious enough for musicians who want to experiment. He told me that too many jazz bars/clubs in Tokyo cater to only one kind of audience (older/richer) and that he's trying to bring in a different kind of crowd. The Friday 'New York Jazz Room' nights featuring a regular group of formerly NYC-based Japanese musicians is well worth dropping in for.
The vibe is warm and friendly at V Mood and the space large enough that you can move around; the big glass doors opening out onto the street give it a real different feel to most claustrophobic jazz joints. I was very happy to find Vanilla Mood, it's a groovy jazz spot in Roppongi that you can escape to if your friends are heading to some meat-market/awful-music club.