Nadja is a great little cafe in Koenji that stands out for its tasty lunch menu, especially the Malaysian style curry.
Kissa Seikatsu (喫茶生活 "Cafe Lifestyle") is a gem of a place a few mins walk from Higashi-Koenji station on the Marunouchi Subway Line.
吐夢 (Pronounced "To-mu" or just "Tom") is unique in a couple of ways.
Stardust is an old bar, first opened in Asagaya in 1971 by the very chatty Masuda Junko-san. It's been at its current spot for about fifteen years and has a steady regular customer base.
Tiny club in jazz rich Asagaya, Manhattan is always worth stopping by. All-night jam sessions three times a month.
Rooster is a great little live-house that features jazz, blues, funk, New Orleans..basically all the best stuff.
Aketa No Mise("The Open Store) is out in west Tokyo, not far from Nishi-Ogikubo station.
Meg is a small cafe/club in Kichijoji, western Tokyo.