If you are science minded, the Deutsches Museum is a must-see. Take the S-bahn from the airport to Isartor and follow the signs. English language guidebooks are available in the vending machines.
Drink beer from the source at any number of sidewalk cafes and if you are looking for a cheap place to stay, the Mercure has several places that are quite cheap, including downtown right by Marienplatz and the Frauenkirche. The Hiltons are really nice but can be pricey.
MUC is my favorite city. Its too bad that the new train is not up and operational yet.