I tend to book my Prague accomodation through http://www.a-prague.com/, from the list of hotels you certainly find accommodation. I was very pleased with their service in helping me find the best match for my location, space and price needs.
I have the same experience with http://www.charming-prague-hotels.com .
They are really quick and helpful and the you are quite sure what you book due to their map!
Looks like you already have several options but also, the Hotel Adria in Prague is quite nice. It is on Wenceslas Square with sound-proof windows and has a great restaurant that looks like a grotto. Not sure what the prices are now.
My sister-in-law stayed in Budapest last year, on a very tight budget. Odd - because she has quite good taste and wouldn't stop just anywhere, don't know how she does it.
Will get her to join on here and share her secrets.
:o)
My friend had gone to New York last week. I remembered they were also finding such type of difficulty in finding hotels. At last they prefer the LastMinuteTravel site for booking their hotel and they got very good deal as well as good location of hotel. It was very near to all spot and they enjoyed lot of in their tour.
The Pension Prague City is situated 10 minutes walking from the Wenceslas Square in a quiet place of Prague. Budget accommodation in room with en-suite bathroom, pension U Hejtmana is a pretty good accommodation in a good price situated in a quite area in Prague - Zizkov, within walkable distance to the main historical centre.