I loved Prague for beer for three reasons:
1) The beer is cheap
2) If you want another beer, you just give the barman a thumbs up and he brings you another
3) The "bar snacks" are fantastic - massive portions and low prices.
I have two bar recommendations (based on a weekend trip several years ago, so memory is a bit sketchy).
First is Tretters. Not beer at all but a great cocktail bar and not expensive. Great if you're over there wooing someone. Not one for drinks with the lads really.
The second is vkolkovne.cz which is just around the corner from Tretters. This place had massive plates of food and sold a light beer and dark beer that they would mix half-and-half if you wanted something in the middle! It's probably a bit of a tourist trap but was just an easy place to get on with.
Might also be worth peering in the window of Lokal (
http://lokal-dlouha.ambi.cz/en/). I honestly don't remember much of the place as I'd had quite a few beers by then but recall it having something of a traditional beer drinking hall vibe, with some fairly hearty grub.
BTW, might be worth doing a search as I think there was a similar thread about a month ago. There's a forumite who lives/d in Prague who will probably be able to shoot down all my suggestions and point you to some better places!