Personally, I'm with dhammer53 here and would go to Prague. However, it could depend on what your interests are. If you like museums, classical music, coffeehouses and pastry, and a more formal feeling, go to Vienna. If you like history, beautiful old buildings, beer and a great walking-around city, go to Prague. Both the Jewish Quarter and Prague Castle are fascinating. Oh, and they have very good pastries in Prague, too.

P.S. dhammer53's Prague trip report is excellent! ^ I referred to it when I made my trip last September.