Which city should be better as base camp, Munich or Salzburg?

We spent 4 days in Munich with a day trip each to Neuschwanstein and Dachau included. We spent one day in Salzburg and felt that, for us, this was a good amount of time in each but you need to base this decision on your own interests i.e. Sound of Music Tour. There is a wonderful evening bike tour of Munich, with a stop off at a beer garden, that is great fun! We are an active couple in our mid 60's and would recommend city bike tours as a wonderful introduction to any city. We include these in our travels whenever they are available.

Neither is a good base for all of what you have planned. And you don't have enough time for everything on your list for two full days and fractions of another two.

You don't say whether you will have a car, which will shorten your travel times, but even if you do, Tom is correct: 2 full days plus 2 half days is not nearly enough time for all you have on your list. Look at a map and figure out travel times (by car if you'll have one or by public transport and/or organized tours if not). And then figure out what you're willing to cut.

I would make the choice about where to stay based on which city you'd prefer to "come home" to in the evening and which day trips you're willing to cut. If going to Neuschwanstein is an absolute must, staying in Munich makes sense. If you're unwilling to skip Hallstatt, you'd be better off staying in Salzburg. I doubt you can hit both of these and also spend any reasonable amount of time to get an experience of both Salzburg and Munich.

Unless... if you're driving from Vienna, you could make a detour to Hallstatt on your way to Salzburg. Then spend the first night in Salzburg and do all your Salzburg activities on the first full day. Spend the second night there, then get an early start and head to Munich. Spend the day and night there, and then head to Neuschwanstein on your way to Mürren. This is a compromise that gives you very limited time in Munich, but you will have to compromise on something to make this work. And if you're not traveling by car, I don't see how you could pull it off.

Definitively I know I have to compromise something, my first option to take it off the list would be Hallstatt but the 2 'must do' in the list are apart from each other. So based on this I think Munich is the best bet.

Do you guys recommend any accommodations in Munich? We are planning to use public trans (metro, trains)

I don't believe that you have enough time to see all sites on your list. I'd focus on Munich. You can take a day trip to Neuschwanstein Castle by train. The rest of the time should be in Munich. It's such an interesting city with numerous sites. Have fun! P.S. You can save on train fare to Neuschwanstein by buying your tickets a week or two before you travel. Also the train departure times have an impact on fares. Go to the German Railway (DB) website for more information.

In 2015 I stayed at one of Rick Steves recommended hotels, Hotel Blauer Bock, http://www.hotelblauerbock.de/?lang=en. We needed a hotel with a parking garage for my sons vehicle. It met our needs & breakfast was included. We left the car in the garage and either walked or used the public transportation to hit our sites (BMW Plant, Viktualienmarkt/Beer Garden, Hofbrauhaus).

Enjoy your trip.

I've stayed twice at the Hotel Laimer Hof in Munich. This is a family run hotel and you'll feel very welcome. Check the website www.laimerhof.de for details. This hotel is in a comfortable neighborhood. near the Nymphenburg Palace. The public transportation system is excellent and the day passes make it very easy to move around the city.

Yes, base in Munich.
Neuschwanstein (and Hohenschwangau) and maybe a stroll around charming Fuessen is one full day.
Stroll some of Salzburg (it's compact old town) and the SOM Tour is the other full day.
The 1/2 days stay in Munich.