At least one night you gotta try the U Tri Postru (The 3 Ostriches) right at the Castle side of the Charles bridge. As others have said, why go to Praha and avoid the history?

I stayed at the Intercontinental Praha for my business meeting and it was fine, but after the meeting I went to the U Tri Postru and will never forget it.

Other Praha highlights include the restaurant U Svalta Ducha (The little Church) which is AFAIK the only non-smoking restaurant in Eastern Europe. Great food too which isn't saying much since every half-way decent place in Praha has great food. My other recommendation is Peklo which is underneath the Monestary in an ancient beer cellar.