It really depends which shop you visit. If you try something at the centre they tends to be better supplied but are far from cheap (at least from my perspective).
Example of this is:
http://www.fotoskoda.cz/kontakty/
They have rather extensive second hand department.

If you are after gear and are willing to carefuly inspect the goods, try this one:
http://www.fotopazdera.cz/kontakt

But if you are after cheap films or papers try this guy:
http://www.befoto.cz/kamenny-obchod/
One of the cheapest brick and mortar shops in Prague. He has the same prices as fomaobchod.cz and also usualy has some expired film at very nice prices.