Prague is just so beautiful. I really enjoyed my time in the city. I went there with a friend in 2003, spent 8 or 9 days there. Granted, that was a bit too long to stay just in Prague, but we took our time wandering and did two day trips as well.
+3 for Sedlec/Kutna Hora. The town of Kutna Hora is neat as well - once the silver mines closed, the town kinda froze in time, so it's very quaint. They did offer tours of the mines when I went there in 2003, not sure if that's still the case now.
This is still one of my favourite pics of all time, taken at the bone ossuary:
I also did a trip out to Karlsteijn castle - about 45 minutes outside of Prague, I believe? The tour was okay, nothing outstanding, but the castle is a neat site.