Two days is not a whole lot for Munich, so you probably need to prioritize... and without knowing your specific tastes, it's kind of hard to make recommendations for you. For a good overview of the sights, check the Wikipedia article on Munich.
But, if the weather holds, definately try to have a meal at one of the outdoor beer gardens. Some of the more well-known locations are by the Viktulienmarkt, and by the Chinese Tower and Klienhesseloher See in the Englischergarten.
Many people might recommend Mike's Bike Tour of Munich (and you'll see the advertisements everywhere)... but with only two days, I probably would not recommend this. Although I enjoyed the tour, the guide just takes you by many sights, not actually in them. Spend your precious time inside the many museums, palaces and churches. If large markets interest you, the Theresienwiese (location of Oktoberfest in the fall) hosts a particularly interesting mix of merchants in April.
The trip to and tour of King Ludwig's castles at Schwangau takes the better part of a full day from Munich.