Yes, some excellent Prague advice above. We went recently and it is a great city.
Would highly recommend the following, some of which were already mentioned by @956 Worldwide:
Taste of Prague Foodie Tour - these guys are awesome and it's a fun way to eat/drink your way around; we hit several of the spots mentioned in this thread
Nase Maso/The Real Meat Society/Kantyna - all great meat-centric places
Strahov Monastery - think this is different than the one mentioned above, but unbelievable libraries/ceilings and great beer garden
Kuchyn - agree with this rec for sure; cool at night when Castle is lit up
Lokal - several location and excellent Pilsner Urquell
U Kalendu - great dinner spot
Hemingway Bar - again, solid rec above; good drinks, nice setting and friendly staff
Spanish Synagogue Concert - saw Hallelujah concert here and it was good
We also hit Vienna on the same trip and really liked:
Zum Schwarzen Kameel - cool cafe and good people-watching
Musikverein - excellent historic music venue; saw Vienna Philharmonic and it was impressive
Schloss Schonbrunn - a must see
Nussdorf - nearby wine/Heurigen area; go to Mayer am Pfarrplatz (at Beethoven's home)
Cafe Frauenhueber - neat old cafe; kinda somber/quirky, but the real thing
Vienna Sausage - sounds ridiculous, but great place for a dog on the Ringstrasse
Prague and Vienna were different in many ways, but both great places to visit and way too many great/fun places to list here. Clean, beautiful architecture and friendly people. I want to go back someday for sure. Have fun.