Prague and Budapest are both must-see destinations, they are loaded with sights and require at least 4 days to throughly explore.  Nightlife is excellent in both, but escapeing the other tourists may prove impossible. 
 
Berlin and Belgrade are known more for their atmosphere than sight-seeing, you could see the main attractions in a day or two, or spend several days enjoying the laid back cafe culture. 
 
I haven’t been to Bratislava or Zagreb, they are smaller, less popular cities, shouldn’t have as many tourists. 
 
Other suggestions:
 
Vienna is in-route, but its another large city with lots to see and needs a lot of time to get the full experience.
Sarajevo and Montenegro get high marks only everyone’s list.
Wroclaw in Poland is somewhat undiscovered by the mainstream tourists and backpackers, but extremely rewarding. 
 
 
 

I really wish i could make it to Sarajevo on my upcoming trip… despite the crazy shit that went on there it still looks like a beautiful place. Hopefully I can make it there one day before the next war…