Not so much what to buy, as when to buy it. I'm often caught out still in Prague, but all over the Czech Republic 'ordinary' shops close on Saturday at noon. If you are staying in a hostel and planning to buy in a few supplies for late night snacks, early breakfast or a packed lunch for hiking, make sure you get to the shops on Saturday before noon!
There were quite a few glass/crystal shops in Cesky Krumlov, since this region is famous for its glass. In this store, however, the shopkeeper was more attentive than in others. We were looking for a particular glass and she went out of her way to help us find a good substitute when she realized that the one we wanted was out of production. She was also very helpful when we asked about the Global Tax Refund. She wasn't put out at all by the idea of filling out the forms; she let us know what the minimum purchase was so we could select 100 Crowns more worth of merchandise and get the refund.
What to buy: Glass, glass, glass!
What to pay: I think almost everyone in town charged the same for similar merchandise, but I can't remember exactly what the prices were since everything was in Crowns. (Sorry!)