Prague's unmissables are:
Strahov[/url:3lxzjsgg] (especially if it's sunny)
Pivovarský Klub[/url:3lxzjsgg]
Beer Museum[/url:3lxzjsgg]
U Medvídků[/url:3lxzjsgg] (I'd recommend two visits: one for food and tankove Budvar in the main dining rooms and one to drink in the in-house brewery upstairs at the back).
For the serious beer geek who doesn't mind leaving the city centre there's Zlý Časy[/url:3lxzjsgg] and its attached off licence Pivkupectví for take-home bottles. If you want the lager favoured by people who know their lager, the Kout na Šumavě range are on tap in U Slovanské Lípy[/url:3lxzjsgg], the brewery's Prague tap.
U Fleků's worth having one in just because it's a landmark. It's very production-line touristy, though.
For food, if you're into steak don't miss Čestr[/url:3lxzjsgg], just beside the National Museum at the top of Wenceslas Square. They have tankove Budvar too.
There's a good and inexpensive pub guide[/url:3lxzjsgg] available, and there's some stuff on my blog from my trip in March here[/url:3lxzjsgg], here[/url:3lxzjsgg], here[/url:3lxzjsgg] and here[/url:3lxzjsgg].
Bratislava has a couple of brewpubs. Scoopergen has a map here[/url:3lxzjsgg]. I liked the Slovak Pub for its food and the tankove Zlatý Bažant.