I was there in July and ate at Lokal from that NY times article, definitely worthwhile. Mostly of course, I drank and for that I recommend Hemingway's Bar (make sure you go here), Bugsy Bar and Bar & Books all had great cocktails and bartenders. Also there is a monastery the name of which escapes me on top of the same hill as the Prague castle where they brew their own beer and serve really good traditional Czech food.