In Memoriam, FlyerTalk Evangelist
Join Date: Jul 2002
Location: Durham, NC (RDU/GSO/CLT)
Programs: AA EXP/MM, DL GM, UA Platinum, HH DIA, Hyatt Explorist, IHG Platinum, Marriott Titanium, Hertz PC
Posts: 33,857
It's a tough call, they're both great cities and I enjoyed them both almost equally. If I had to give one an edge it would be Prague, but only slightly. Look at it this way, either one you pick is going to be a good choice.
I echo others who say Vienna is skippable or can be seen quickly.