You could do a lot worse than stick pins in a map.
If you're heading Munich way, Salzburg is good for a day, Nuremburg is a decent stopover en-route to Prague, Switzerland/Vaduz are both really cool but overpriced and not really 'value'.
If you're heading South-West, Trieste is a surprisingly nice City and Ljubljana is by far the nicest city in Yugoslavia. Zagreb is crap.
I've never been to Budapest, but nobody's ever been there and not liked it (that I know anyway).
Vienna is like Germany, but without the Germans and much nicer for it. Speaking of staying in Germany- visit Berlin, it's good. Bratislava had a nice chilled out feel.
I'm a big fan of Poland. I'm pretty sure you can get a sleeper train from Berlin to Warsaw. I'm planning to visit Krakow sometime soon, not sure when exactly.
Erm...I'll maybe add to this some more when I think about it.