The guys and gals over at Tokyo Food Page have a wonderful page listing a great deal of Beer Pubs and Beer Bars in Tokyo with reviews for your beer loving pleasure. Go take a look!
Belgo in Shibuya is a personal favorite. The tree-house sitting is the best!
Shibuya / Belgian rest/beer bar
Shibuya 3-18-7, Shibuya Ichigokan Bldg. B1F. Open 5:30pm-2am. Closed some Sundays.