I just returned from Europe and was in Munich for 4 full days as well. Here was our itinerary so you can get a feel for activities
Day 1
Arrived at hotel next to train station at 12 noon. Spent some time in Marienplatz and the market then took the S train to the BMW welcome center. My daughter is 16 and just got her license so she wanted to go. I really was a cool place. We didn't go to the museum, we just stayed in the free area. Lots of new and old BMW's to see. I was pleasantly surprised. Afterward, we walked to the Olympic Park
day 2
Took the Dachau Tour with Radius Tours. Very moving. Do not miss. I think the tour left at 10:30am and we were back around 3pm. We decided to take the 4:30pm Bike tour with Mike's Bike Tour. At the start of the tour, my wife and mother-in-law freaked out with the bikes and so it was just me and my daughter. The bike tour was really nice. We saw a lot of the sites that most people walk to and were able to see a lot of the English Garden. The highlight was stopping at the Chinese Beer Garden in the middle of the park for beer and dinner. there had to be 5,000 people there since it was the beginning of the World Cup. the beer and pork knuckle was excellent. Great bonding with my daughter since I let her have her 1st sip of beer. How many of use could say our first sip of beer was in an authentic beer garden. Of course she hated it but it was a great experience.
Day 3
We took a bus tour to Neuschwanstein and Linderhof castles with Grey Line tours. Both were great and do not miss experiences. However, to get it all in, you only have a short period of time. There was a short 30 min stop in Ommeronagou (misspelled). This town was very cute and we would loved to have more time here and at the castles. I would make two recommendations. The first would be to rent a car and leave early in the morning so you could have more time at the palaces and Omm. or do the same but spend the night so you can really have more time without all the tour crowd. The drive once you got out of Munich was very simple and well marked. With a good GPS you should not have any trouble.
Day 4
Since my wife and Mother-in-law didn't see the sights that we saw on the bike tour, we revisited most of them and spent more time visiting the Residence Museum. This didn't take long so we took the s train to Nymphenburg Palace. The palace was ok. If you haven't seen a lot of palaces this it is worth the trip. If you are going to Vienna or Paris, then pass on this and spend your time at the palaces in Vienna and Paris.
If we didn't have to back track some of the same sites that we already saw on day 2, then we could have done a one day trip to Salzburg or Eagle's Nest. Salzburg was very nice and we went there for 2 night after we left Munich. We spoke with a lot a people who did this as a day trip from Munich and they felt it was worth it. It's a easy train ride about 2 - 2.5hrs depending on the train.
With all this being said, I should have told you that we are not museum people, we are more the old building and history people.
I hope this helps. Of course, this would fill up the days which allows plenty of time left for the Beer gardens. The hofbruhaus was great but very touristy. I really enjoyed the Chinese Beer garden in the park. You felt more like a local.
I hope this helps and have great time.
David