Jikan Ryokou (the sign is in Japanese 時間旅行, it means "Time Travel") is simply wonderful. It's a tiny 12-seat joint in the back streets of Nakano, an area full of small drinking dens.
Rompercicci is a new jazz cafe/bar just a short ten-minute walk from Nakano Station. It's a bright, warm space with superb speakers and an extensive vinyl collection covering all genres.
I found this small-even-by-Tokyo-standards "piano bar" while lost in Nakano one night.
Neighborhood cafe/bar/small live club. This is the kind of place you really only find in Japan; intimate, friendly and wonderful. Live music most nights but it's not really a "club".
Organ Jazz Club: the name gives it away, doesn't it?
Genius is now at it's third location, after having been in Shibuya for more than 25 years.