There's an English Language beer tour or two that pickup at the Glockenspiel and take you around to several breweries for many tastings. I can't remember all of the stops as it was many years ago, but Paulaner, Schneiderweiss, and the Hofbrauhaus are definitely on the tour.
All About Beer's "150 Places to Have a Beer" lists:
Augistinerkeller, Spatenhaus an der Oper (opposite the Opera House; good spot for food), & the Hofbrauhaus.
I'm definitely a fan of Schneider's Weisshaus & Ayinger (opposite the Hofbrauhaus).
If you want to get out of the city for a bit and head to see Castle Neuschwanstein (will pretty much take a day), I would highly recommend stopping in Aying along the way and heading to the Ayinger brewery (I regret not doing this). Andechs Monastary is supposed to an absolutely fantastic visit and is 26 miles outside of the city (train, then bus).
Adam