I was in Prague in October 2009 and there wasn't a whole lot of "craft" beer. The corner part eliminates most places I can think of. There is a brewpub Pivovarský Dům on Lípová (Nové Město) that is on a corner. Also Ferdinanda (taproom for Pivovar Ferdinand, which is an older brewery but does brew some "crafty" beers) on Opletalova near Václavské náměstí.

Not quite in the city center, U Slovanské Lípy on Koněvova in Žižkov is restaurant with good beer. I believe sometime in 2010 they changed their name from Koutská pivnice.

Places that had "crafty" beer in 2009 but weren't on corners were places like Pivovarský Klub on Křižíkova in Karlín (related to Pivovarský Dům), Novoměstský Pivovar (a brewpub) on Vodičkova, and the original "Craft Beer Pub" První Pivní Tramway in Záběhlice but you wouldn't forget that one -- not anywhere near the center and literally in an old tram building at the Spořilov tram station.

Somewhere I have my notes from my 2009 visits but we didn't visit a lot of "craft" beer type places, mostly pubs that had beers from some or another regional brewery.