Try
http://www.hostelworld.com
Click 'Additional search options'. Then select 'Budget Hotels' and 'Guesthouses'.
It's a great site but it has one major fault: Even if you tell it that you're a solo traveller it produces a list of hotels which includes many which only offer accommodation for couples or groups. So it can take a while to work your way through the accommodation to find something suitable. However, I've just taken a quick look and I think that you'll find the effort worthwhile. For example, the Prague City Pension is �23.51 per night and the Attactive Penzion is only �21.04 per night. If you're prepared to rough it in a two-bedded dormitory, the Private ILA B&B is only �6.16 per night.
Those examples are just the first few that I found. If you work your way through the list, I'm sure that you'll find plenty more. (Additional hint: When you view the details for any particular accommodation, you can click on the 'Ratings' tab to view all customer reviews from the past 6 months).
Chris