Prague is fantastic. The main old city is fairly compact so you can walk from one side to the other easily.
We went back in 2003, fly drive for the MotoGP in Brno. End of July/early August so really hot and busy with tourists.
The castle was fantastic. The fortified walls contain a church and small village.
We stayed a couple of days when we got there, then toured down to Brno. We stayed at an apartment booked via an agency, it was about a mile out of town and very cheap, it felt safe enough walking back from the town at night so didnt bother with taxis/trams.
We left at 5:30am to get the taxi for the airport, shut the apartment door and pushed the keys through the letterbox as instructed, got downstairs and the front door was deadlocked, we needed the keys to get out
Felt a right twat having to wake one of the neighbours. Looking at the names on the letterboxes another apartment had the same name on it, so hoped the flat we rented was theirs as well, so woke them up.
Like Dead Eye, I like these places in winter away from the crowds. Vienna is a good short stay break, easy to get to from its airport. Its a bigger place, but has an excellent metro. I combined it with a 2 night stop in Bratislava, 1 hour away on the train. Small old town, but very atomspheric, and beautiful women, everywhere. January, and cold and a little rain/snow but uncrowded.
On another trip I combined Vienna with Budapest, 3 hours on the train. Impressive city, still has a lot of original stock on its metro by the look of some of it. Amazing old open air pool with water at 28c, locals playing chess. That was in March 2011 and had fantastic weather, like the UK had that spring.
As with all big cities, watch out for pickpockets. Otherwise all the above felt reasonably safe so long as you stay away from the obvious rough areas at night.