U Fleku is pretty classic. Sure, it's filled with tourists, but it has fantastic beer and hearty Czech food - and I haven't been there since 1993 - but it's been around for many hundred's of years so it probably hasn't changed much. The beer is some of the best I've ever had. U Kalicha is also great, but even more touristy (but German tourists) what with the Svjek association.
Aromi- Manesova 78 Praha 2- 420-222-713-222- Great Italian restaurant. Food was great, staff was great and the deocr is great. Interesting tableside presentation of all of fish specials of the day. Fried scmorza cheese with proscuitto and pumpkin ravioli with clams were excellent. Cappuccino creme brule with cantucci cookies was pure heaven. Take the green metro line to the Jiriho z Podebrad stop. As an added bonus the Prague tv tower is in the same area which we went up for some beautiful views. Tower open until 11pm. Lost receipt but I remember Aromi was a good value.
I had some great meals a few years ago at the Restaurant 7 Angels, Jilská 20, tel (02) 2423 4381 (obviously I saved their card). If I remember correctly it was off the main square where the big antique clock is.
Just be careful (in general, not just here) to ask how much a bottle of wine is before you order it. Typically in Prague there is no wine list as such, they just bring out a few bottles and ask you which you'd prefer. Prices can vary astoundingly!
Also, and this may no longer be true but was a few years ago, beware of scams where a restaurant will post a prix fixe dinner menu, but not bother to tell you that it applies only before 7PM or some such, and when the bill comes it's many times higher than the prix fixe.
Don't get me wrong, it's a great city for chowhounding, but you need to be a bit more cautious than in most Western cities.