Before we rented our flat in Vilnius, we checked out places on line, but the prices are all geared to expat business people with expense accounts, so most likely anything you'll find on line would be overpriced.
We found our place (in the Old Town, for about 1/4 of the on line prices) through a friend of a friend, which is definitely the way to go, if you can stand to wait until you're there to make your decision.
If you're willing to stay out of the centre or in a less modern/renovated/desireable building, you'll probably be able to find something cheap, but anything historic, redone or central will likely cost a pretty penny. If you can wait til you get there, learn the Czech for "To Let" and check out any signs in windows you go by, look in the local papers (then you'll pay local, not expat prices) and ask hostel staff or any other locals you meet, of whom you'd feel comfortable asking the question.
If you must book something in advance, check out "Prague in Your Pocket" (order one from www.inyourpocket.com
, you'll definitely need the full guide, the on-line version isn't as comprehensive, under "Apartments/Private Rooms". They often have short and long term listings and usually a good range of prices, decent quality and often quite good locations.