We stayed last year at the Pension Dientzenhofer, in Mala Strana.
The house is 16th Century and has an interesting history, being the birthplace
of the great baroque architect, Kilian Dientzenhofer. Just a small place
with two suites, three double rooms and a single. Not at all glitzy but
prices then were 3,800KC for the suite (Bed &Breakfast) and 3,500KC for
a double room (B&B). We tried both, as the place was full for the nights
we were there and the front double which is a recent addition was the
better option than the suite in the main house, which was quite spacious
but had very little charm. A slight disadvantage to the former was the
location near the entry gate to the courtyard but that didn't bother us
too much, given the small numbers of people coming and going.
At that time, the conversion rate to Australian dollars was $167 for the
suite and $154 for the double - which would make it around $US85 and $US72
I'm sure there are cheaper options - and there are certainly more expensive
ones - but we enjoyed the locality and the back street location was sheltered
from the madding crowds while still only a few steps from the main thoroughfare.
They also provided a car to meet us at the station at what seemed a reasonable
rate and which made the initial orientation easier.
There are numerous web pages with accommodation in Prague.
As a start, you could try:
Also take a look at the Czech Republic Consular Information pages on http://travel.state.gov/czech_republic.html
and the Lonely Planet Guide at http://www.lonelyplanet.com/letters/eur/cze_pc.html
Best of luck,