Vienna: I did went to see the Spanish Riding School to see the horses perform which was amazing. For a much less fee you can see the horses being exercised. Either way, check this out to see if this is something you are interested in.
The subway and trams are excellent forms of public transportation.
Munich: Nice city, liked it well enough and would like to go back, been a few times now on tours. Great beer halls, easy to walk around, lovely shops, Main square is the Marienplatz not to be missed and the Glockenspiel. I stayed two times right near the Viktualienmarkt which is very nice to walk around and see. I loved the Residenz, not to be missed, which is the palace right in the city! I went to the Hofbrauhaus which is a fun place to go for drinks one night. I went to the Neue Pinakothek museum of 1900-1920 paintings which I loved!!! I am a huge museum fan. I did not go to the Alte Pinakothek which I know is very highly recommended and I want to go to if I get back to Munich. It was being renovated so I opted to see the other museum. No time for both anyway. There are some main churches to see, St. Peter's, St Michaels which I saw the time before this year's trip. Churches are always impressive, so go see all of them if you can. I also went to Dallmyr Delicatessen which has a lovely restaurant on the 2nd floor, good food and nice elegant atmosphere. I wore slacks or jeans not needed to get dressed. I went for lunch, would go back!
I did not spend as much time in Munich but hope to get back to see the other museum and would see the two palaces again.
Salzburg is next to tell you about. I was there briefly on the tour but enjoyed this city and would like to go back.
You will find wonderful architecture in both Munich and mostly in Vienna! The food in Vienna was excellent ( spent more time there) and you will be "hiking" just by walking every where in both cities, I assure you of that!