i also found in eastern europe that at times it was easier (and cheaper) getting a bus.
Not to mention - sometimes faster! For instance, going from Prague to Cesky Krumlov (and back) is faster by bus than by train, because it's direct.
I stayed at the Golden Sickle in Prague - not too impressive, but cheap and super central. The Hostel 99 in Cesky Krumlov was pretty sweet. It's at the edge of the town near the bridge where the kids entered the town in 'Hostel,' so it's really close to the bus stop, and the accommodations are pretty nice.