I did a similar trip between Prague, Krumlov, Salzburg and Vienna, with a few other stops in between, by bus and train. We saw a lot of things by just walking around and using local transport lines, which include stops in the middle of nowhere. The area between southern Czech and Salzburg is just amazingly beautiful. Of course, Prague and Vienna are also amazing cities to visit, but that everyone already knows.

We only caught trains in Austria, and they were extremely punctual!