I have been to a number of the cities mentioned so far and all are excellent. My brief thoughts on each:
Vienna - Vienna is wonderful. The buildings are fantastic and it's a lovely place to walk around. You can see the rich history that the Austrian-Hungarian empire had. It's a very wealthy city which is reflected in the type of shops you see, the buildings you see but also the cost of things like accommodation, so worth bearing in mind. The Schobrunn palace is stunning with fantastic gardens and a large zoo.
Budapest - Loved Budapest. More great buildings, wonderful climate and a rich mix of Soviet history blended with modern buildings and older buildings too. Soviet designed subway system is interesting and the view from the castle overlooking the river Danube with the awesome parliament building on the other side is unforgettable. Accommodation generally much cheaper than Vienna.
A useful point is that Budapest and Vienna are very close and easily reached from each other in 2-3 hours by fast train. Therefore consider doing both in the future when you've got a bit more time to spend?
Prague - I have no interest in drinking/clubbing/whatever but Prague offers so much more than that. Lovely buildings and a fantastic views again from the castle. Great place to chill out, plenty of nice bars and restaurants. You can also get epic deals on accommodation - I think I paid something ridiculous like £35 a night for a Marriot right by a subway station 10 minutes from town.
Munich - Very nice but unless you have specific interest in some of the major attractions Munich has - for example BMW World - then I'd question its choice as a city break destination before you've sampled the others in the list. It's lovely but there is more variety and more memories to be had elsewhere.
Berlin - This would be my choice in Germany for a weekend city break. Another of Europes great cities. The cold war history is amazing and there is so much to see and do.
Paris - Don't bother. After years of wanting to go I finally made it in February. And very nice it was too - as everyone already knows - but it's SO expensive. It's not that I mind spending the money but the same amount of money goes so much further in pretty much every other city in Europe.
If you have never been to any of these cities, I would pick either Berlin or Prague first
Also don't forget closer to home. Edinburgh is particularly nice and has as much appeal as some of those in the list above.