I'd definitely recommend the following hostels according my personal experience:
Cesky Krumlov: Krumlov House , only 25 beds, a cozy atmosphere, wooden curving decorations and a lovely owner.
Prague: Sir Toby's is a must, not a small hostel but very good facilities and excellent services, when I visit Prague, I always stay there.
Bruges: Hostel Lybeer, about 50 beds, a typical old-style building, themed nights, an authentic setup for the early 1900's, and also a very good host who can tell you anything about Bruges.
Split: Hostel Split, 15 beds, run by an aussie chick, a lovely small hostel in a lovely small city.
If you are looking for small hostels, I'd recommend small-hostels.com or just ask uktrail for hints! ;)