Just to add to the too-late recommendations, for posterity:
I spent a week in Berlin last fall and searched out what breweries I could when not occupied by work and sightseeing.
http://www.hopsandbarley-berlin.de/ Was a cool little place, watched a bit of the football match there. Good beer, local styles. Adjacent neighborhood and Warschauer Straße U-Bahn station can be a bit sketchy.
http://www.lemke.berlin/ Really cool location near Hackeschen Market, under the U-Bahn tracks. Good food, with a little bit of a traditional bierhaus atmosphere. Beer is largely American craft styles, decent but not great. I found the imperial IPA and stout in particular to be rough around the edges.
http://brauhaus-georgbraeu.de/ Traditional brauhaus in a restored building across the Spree from Museum Island. Lots of tourist traffic. Traditional German beers and food, all good stuff.
http://www.vagabundbrauerei.com/ Cute little bistro-style tap room in a residential neighborhood, bit of a walk from the U-bahn. Limited selection of house and guest taps. Is run by ex-pat Americans, styles trend towards American. I remember the saison being good, not much impression of the others.
http://eschenbraeu.de/ Funky little braukeller, close-ish to Vagabund. A little hard to find, you have to enter the courtyard of an apartment building; follow the signs. Hours were a bit odd. I remember the weissbier being tasty, as were the pretzels.
http://www.pratergarten.de/ Lovely biergarten and restaurant. Great food, local beer styles. I remember the house beer as good but not remarkable.
http://www.pfefferbraeu.de/ Best. Damn. Burger. I. Ever. Had. German beer styles, OK but not great. Really nice building. Bit hipster, really.
http://kaschk.de/ Coffee and beer bar with a wide selection of craft beers. Great staff. Shuffleboards downstairs.
http://www.alt-berliner-weissbierstube.de/ Touristy, traditional-styled restaurant near Alexanderplatz. I stopped here because I got a recommendation online as a place to stop for Berlinerweiss mit schuss. They served me Berliner Kindl out of the bottle, which was fine. Achievement unlocked: drank Berlinerweiss in Berlin.
Sigh... Now I really want a German bretzeln. So good, nothing like it in the states.