Do a search on chowhound.com for these cities - you should get tons of info from people that really care about their food! Don't miss Viktualienmarkt in Munich - Weisswurst & Bier - the Breakfast of Champions!! Haxnbauer is also very popular if you like roasted pork shanks or other Bavarian delectibles.

Actually, come to think of it, the Innenstadt around the Hofbrauhaus is going to be crazy with fans, so I would look more in outer suburbs, or Schwabing, which, honestly, is always crazy, but hopefully all the yahoos will be at the HbH.