We were in Prague in April 2002. It's now very much a tourist place, and there are plenty of restaurants to choose from.
The first evening we went for an excellent meal in a rather upmarket restaurant whose precise name I can't remember but which included the Czech word for "rose" (this was on my birthday, and we wanted to splash out!). We read about it in a free city guide that we picked up at the hotel, and liked the description so we decided to give it a try, and it was absolutely fantastic.
The next evening we went to a restaurant in Wenceslas Square which served local cuisine and was full of locals - but again, I can't remember the name.
A word of warning - although we didn't experience this (as we were there mid-week) I have been told that Prague tends to be full of rowdy Brits at week-ends (as it's cheap to get to thanks to Sleazyjet, and famous for cheap beer) - so mid-week may be a better time to go.