I have some suggestions for other towns to see in Czech Republic. The one town I can speak from personal experience is Olomouc. It is much smaller than Prague (about 100,000 in population) and is very cheap. The center of the town is beautiful and it has some interesting things to check out there (a bar in an old airplane). It is about 2 1/2 hours from Prague from what I can remember. I would suggest this place.
Some cities that I have not been to but have heard a lot of good about. One is Cesky Krumlov. There is a fantastic castle there and it is starting to become a popular stop for backpackers. Another town is Karlovy Vary which is more of a resort town, but it is supposed to be quite cheap as well and very nice. Of course, what you like to do will depend on what towns are more to your liking (partying, seeing sights, museums)