We will be taking the Munich, Salzburg, Vienna tour beginning Dec. 3. We are planning to go from Vienna back to Munich for a night. We are thinking about going by train rather than flying. Any comments or recommendations about the route to take or places to stop at along the way?
Not sure I am following. If going by train (about four hours), you do not stop nor have a choice of routes as the train only goes one way. You cannot get on and off the train along that route. If you are just returning to Munich for a plane home, why not fly home from Vienna and enjoy another day in Vienna. I am sure I am missing something in your question.
I did that tour in Dec. 2017.
Flights from Vienna back to my home airport, Phila. (PHL) were expensive and left Vienna crazy early, so I took the train back to Munich, then flew home the next day.
There really isn't a choice of route, and probably nothing worth stopping at in December that you won't have seen already on the tour.
BTW, it snowed while we were in Hallstatt--magical!