i used to go to Munich a lot, because I lived a lot closer than I do now. There's so much to do it amazes me that people think they can see the city in a couple days. Just the list of museums I like would take weeks to see.
The Deutsches Museum - How good is this? I took my boss one time (he was an engineer) and it was all we could do to get him out of the place 6 hours later. I've spent days in this place over the years.
The Alte and Neue Pinokothek's - two of the greatest art museums in the world. Major museums worldwide (the Smithsonian, the Getty, the Met, etc.) lean on them for the temporary exhibitions they hold.
The Residence - I've never taken anyone here and left in less than 4 hours.
The Bavarian History Museum - My second favorite German history museum (behind Nurembergs).
The Egyptian - I prefer this to the collection at the Louvre.
The Transport Museum - I like cars, and trucks, and etc. (which leads to...)
The BMW museum - Fantastic collection, very interesting architecture.
The Glyptothek - rarely visited by tourists, and yet a fantastic collection of Greek and Roman statuary.
The Hunting and Fishing Museum - I love this place, and how it stays open I'll never know, as it's not visited often.
The Toy Museum - What can I say; all the stuff I wanted as a kid, and more. Brings back memories every time I visit.
The Palaeontological Museum - fantastic collection of dinosaurs, and when combined with a visit to the Minerology Museum it's enough to make a Geologist ecstatic
The Staatliche Antikensammlungen - Neoclassical architecture and a great collection of antiquities.
Nymphenburg Palace - In good weather it's worth a visit just to walk the gardens.
The Haus der Kunst - in the 1980's this was a bombed out shell, sitting on the edge of the English Gardens. Now it's a good art museum. I go there just because I like to see the changes.
Beer and food - I won't visit the Hofbrauhaus or even the Ratskeller any more as they're too jammed with tourists and expensive. The Spatenbrau Haus (across from the Opera) has (my opinion) better beer, but it too becomes uncomfortable these days. Schneider's (by the Rathaus) is always good. There are also several Augustiner places (I like the one by the Hunting museum). And the Lowenbrau Haus is far enough away that it still gets as many university students as tourists. Good beer and food there. But I also have a tendency to pick up something in the victual markt (fleischcase for around 2 euro is a great snack), or at an Imbiss. Look for a place where there's a line of German students, the food will be good and cheap. In warm weather look for a beer garden north of the old city center.
I normally just use the Marriott properties these days, since my favorite pension became a bank when the owner retired. Just don't stay on the west side near the train station; much better to look north of the old town around the University.