I like Petrin Hill too. You can take the funicular up (there's a decent restaurant halfway up too with good views), walk around and if you have the stomach for it, climb Petrin Tower. It's 300 steps and designed similar to the Eiffel Tower...amazing views from the top.

If you're interested in war stuff, the Czech Military Museum is quite good (and free!) and this is a really moving place to go:

http://en.wikipedia.org/wiki/Church_..._and_Methodius