Anyone stay at Hotel Julian. Their web looks nice and is a recommended hotel of Steve Rick.We will be there 4 nights this coming Sept.
If you look at this page, which is the Guidebook Feedback for Rick's Prague And The Czech Republic book, you'll see a number of very positive mentions of the Hotel Julian: http://www.ricksteves.com/books/feedback/static/290_2.htm
We stayed at the Hotel Julian for a week and loved it. It is extremely nice and the staff is wonderful. The breakfast was outstanding. If you are going in summer it also has air conditioned rooms available. The only downside is the hotel is a few miles away from old town. This was not a problem for us as we were there on vacation and public transportation was just around the corner. Also, if you are taking any day trips from Prague, Mike's Chauffer is next door to the Julian and they do a great job. They also provide transit to and from the airport, but its a little pricey. If you are in Prague on business rather than vacation, we use the Flora Marriot which is better suited to that purpose.
I highly recommend the Hunger Wall Residence. I had a wonderful experience there. The location was great and the price was affordable. I loved it.