I went on a weeks beer drinking holiday in the Czech Republic over the summer, see if you can get hold of the 'CAMRA Good Beer Guide to Prague and the Czech Republic'. It's got all sorts of useful info in it. Try to avoid the big nasty brewers like Staropramen and Urquell - if you want to try Urquell try to find a 'tank pub' that serves it, they do a fresher unfiltered version which is a lot better than the standard stuff.
My two favourite mciro breweries from Prague were the Pivovarsky Dum and the Medved Brewery (who do an excellent beer called x-33 at 12% abv) Note that in CR beer is measured in balling - the amount of malt sugar in the beer prior to fermentation. So if you see a beer at 12% it's only really 4.5 -5%.
Also the Kvasnicove beer style is excellent, kind of like a real ale. Pretty much all the beers good though especially considering how cheap it is!