Yes here are three of the best...
Wirtshaus Ayingers - Platzl 1A (very near HBH)
Schneider Brauhaus - Tal 7
Augustiner Keller - Arnulfstraße 52
Our hotel was the Platzl- so it was literally out the back door to either Ayinger or HBH. I found that I loved Ayinger the best, and no matter how busy it was, they always had a table for us near the back bar. There were alot of us in the group, and about 12 of us seemed to be in there at any given time of the day or night.
HBH was an absolute zoo all hours, except for one morning around 11 AM.
We visited Spaetan, Schlenkerla (both pub with the owner, and the brewery), Andechs Monastery Brewery, Kloister, Ayinger (in Aying, the brewery), Augustiner (many times!), Weihenstephan (my favorite biergarten, in Freising), Englisch Garten, Schneider-Weisse (huge multi-course beer pairing dinner), Weltenburg Monastery and Brewery, and of course Pilsner Urquell and more in the Czech Republic. It was really the best trip ever, with fellow beer geeks.