http://www.umedvidku.cz/
They have nice, clean, cute, and decent-sized rooms. The staff is friendly. The restaurant/beer hall is also good and convenient. A HUGE breakfast is included, and it has a large variety to keep you full way past lunch.
This pension is in a great location, on the edge of Old Town, but it’s close to New Town. It is also just a block off the river, so it’s very easy to get to one of the city’s many bridges. It is less than a 10-minute walk to the Old Town Square.
It's about a block form a Tesco (where the metro station is located), so if you need something or forgot to pack something, it's easy to pick it up here. Plus, being the near the Tesco, you can buy film and other tourist needs, but at standard prices versus trying to buy film next door to the astronomical clock!
The hotel has "historic" rooms for a 10% higher rate. The basic room I stayed in was very nicely decorated, with furniture I would say has more character than most hotels I have stayed in. At my first quick glance of the room, I asked my friend to make sure we weren't accidentally given an "historic" room. I would guess the historic rooms are pretty nice.
The hotel also provides a computer with free Internet access, which was fabulous.