When are you going? In the middle of summer it's going to be very expensive, how much are you willing to pay?
Do a day trip there is more to see in the Czech Republic than Prague.
I am going (2 adults + one whiny kid) August 28-September 1. 4 nights. We want to pay up to SFr 150 a night (or approx US$150 or thereabouts) and must stay in the town center.
And, we are open to all suggestions outside Prague which are doable without a car (meaning, local transportation). If you have ideas, please let me know or send me a PM or even a good link if you have.