rybarsky klub on kampa island for freshwater fish--trout and carp--all good stuff, good value.
pivovarsky dum on jecna st. for outstanding fresh unfiltered and unpasteurized beer-the coffee and the nettle and the champagne versions are all favorites-plus good knedlo-zelo-vepro.
chudoba on vinohradska for great czech fare and very very good ribs.
u pinkasu at NE end of wenceslas square (in jungmannovo namesti, actually) has a great garden to eat in that shares a wall with mary of the snows church next door--good food and good beer.
in general i'd avoid anything in the old town square or near the castle--you'll pay 3-4 times what you'll pay in the much more prague-y neighborhoods of vinohrady, zizkov, andel, etc. these places are all a 10 minute tram or subway ride from the center.
example: the bavarian sausages from the food stands at the NE end of wencelsas square seem to be a good value for 40 crowns, until you go to restaurants in the above areas and get a plate of sausages, potato dumplings, and sauerkraut for 55 crowns.
that having been said, those sausage stands are great.
ebel cafe on tynska near the old town square has good coffee.
tiger tiger on anny letensky in vinohrady is praised for its thai, if you need a break from dumplings. pizzeria grossetto on rumunska in vinohrady has a great porcini and pancetta pizza they offer in the fall.
have a good trip.