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.
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.
Jazz Olympus was opened by the very friendly Komatsu-san in 2009. It's a sleek cafe/bar that is already well known in the area for it's lunch-time menu (rare is the jazz cafe with good food!).
Small Hours is a new cafe/bar located in the back streets between Ochanomizu, Jimbocho and Suidobashi stations.
Grauers is a new cafe/bar opened August, 2011.
Scratch is a quiet cafe/bar that's been in Kichijoji since 1974. They open during the day for cafe time and have an extensive food and drink menu.
Jazz Nutty opened in 2009 next to the campus of Waseda University. The wonderful Mr.& Mrs. Aoki ran their own flower shop for 26 years before deciding to open their own cafe.
not yet...soon!
Really old looking cafe in the shadow of the Sunshine City monstrosity (er.."skyscraper") in Ikebukuro. More comments soon when I get back for a long visit.