+1 on Pivovarsky Klub, it is not that hard to get to it (less than 100 yards from nearest metro stop), and the selection of Czech darks from smaller brewers is something you won't find easily. Also great food there, and much less expensive than the city center.
Also consider Klasterni Pivovar, in the castle quarter at the top of the hill near the monastery. It is a brewpub that usually has 3 beers on draft--unfiltered amber and dark, and typically a third that might be from another brewing culture. when I was there, the 3rd was Bavarian weissbier, and they were about to put an American IPA on draft (I would have been very interested in seeing the Czech interpretation of this).
Prague was one of my favorite cities in Europe. The architecture and history are amazing, it is relatively inexpensive (though becoming less so), and good people. I also came to appreciate the Czech dark style of beer, which I see very little anywhere outside the Czech Republic. These are fantastic session beers with interesting complexity, particularly the artisan examples we tried at Pivovarsky Klub. This is a hidden gem.