not sure what part of switzerland you’ll be looping around, but luzern/lucerne is a beautiful town nestled in the alps. as for germany, heidelberg, freiburg and tuebingen are classic university towns which are quite quaint. the first is probably the most interesting of the three. tuebingen is a pretty small town, and worth spending a day in. freiburg happens to be one of my favorite german towns. it’s in the sunniest part of germany and is the “capital” of the black forest. if you like the woods, then you’ll love this area. check out triberg and you can see the world’s largest cuckoo clock. although there’s a competing “world’s largest cuckoo clock” in the village next door – schonach (or something like that.)
bratislava, well, i’m sorry hibernicus, but i really wouldn’t call it a good alternative to prague. i live in budapest, and i’ve been to bratislava several times and, well, i’m really not impressed by it. maybe you have to show me something i’ve missed.
I’ll third the motion on Cesky Krumlov.
And definitely Salzburg. If you’re gonna do Austria, I prefer this town to Vienna by miles (or kilometers, as the case may be.)