A lot of good suggestions already. A couple of things worth adding:
The BMW museum is right next to the Olympic Park, so worth doing together.
Augustiner seems to be the locals' beer of choice and the beer hall is nice. I'd put it second on my list after Hofbrauhaus, which can't be beat for festive atmosphere.
Try a doner kabab - seems to be the official fast food of Germany, like a gyro only way better.
Pizza in Munich is pretty good. Can't remember any names, but find a place with good looking pie and it'll probably be good.
There's a bakery/cafe in the Karlsplatz that's one of my favorite coffee, WiFi spots on earth. It's tucked upstairs, and always seemed more local than tourist when I went. Good cappuccino, nice cafe menu and nice views of the best part of Munich if you get a window seat. I believe it's called the Stachus Cafe. I use it like my Munich office.
If you do take the easy train rideto Nuremberg, try the famous brewery/distillery there. I think it's simply Alt Brauerei, but would have to check. It's apparently the only place left that does traditional Nuremberg rot bier, an unfiltered red. It also makes whiskeys and makes different schnapps out of each individual beer - maybe stay the night in town, lol. Don't think they have it there, but find a place with rauchbier (smoke beer), which originated in the village of Bamburg like another 45 mins away. It's like a campfire in a bottle, never saw it in Munich, but did get it in Nuremberg.
Eat Kaesespaetzle mit speck if you find it - German Mac n cheese with bacon. I have dreams about it.
There's a big English speaking expat community, and I've found good info on something like "toytown forums."
Have fun, Munich is great and a lot of good short trips from there if you want to branch out.