+1 for Gambrinus !
Check out Chez Marcel on Haštalská, a lovely little relaxed French restaurant, red-and-white-chequered tablecloth type place, lovely food.
Also Ambiente Pasta Fresca on Celetna - we couldn't believe how good the food was for reasonable prices when we had not so great experiences elsewhere.
Have been to Prague three times and these were the two places that stand out for us!
Accommodation - as a previous poster said, check out the various sites for this but I would advise not staying on Wenceslas Sq., its a bit tacky , think O'Connell St - there are nicer places to stay! We stayed once in Wenc Sq (wouldn't do it again), once in Boscolo (lovely but very pricey and oh my god don't have dinner there, we got fleeced) and once in Ibis in Namesti Republiky - which I believe was owned by our very own Sean Quinn. Ibis was a GREAT location, but basic enough room, bed & pillows were not great but I would consider it again for the location and price. My brother stayed in the Clarion Old Town and said it was great, that might be a good one.
As previous poster also said the tram system is great and
www.dpp.cz/en/ will tell you exactly how to get from A to B by bus, tram, walking combination - it's a great site, so handy for checking out tram stops near a hotel you're looking at.
The bus & tram from the airport into the city is great and very quick for the distance travelled and sssooooo cheap. A 24-hour ticket for all transport is about €1.10, you can buy the tickets at the airport transport desk (no machines unfortunately) or most tobacconists/kiosks, then stamp it when you first board a bus/tram and its valid for 24 hours from then, you don't need to stamp it everytime you board a tram.
I love Prague......just in case you're not getting that......!