We've had a great time in Prague, last but certainly not least thanks to our stay in Vaclav's apartment. The location and accessibility of the building, the cleanness of the sleeping room, the furniture we could use in the room/kitchen/bathroom, and of course the service and friendliness of the host. If we'd visit Prague some other time, we'll definitely book the room again. Also, Café Jen and Restaurant Neklid are really nearby and worth a visit!
Recommendations for the city itself: we spent five days in Prague, well actually four days (three or four days is a good length to visit the city). One day, we visited Karlstejn by train (tickets are very cheap), watched the castle from the outside and did some hiking to another city called Beroun, with a spectacular viewing point halfway. Something else I suggest is climbing the hill to the east of the Florenç bus station, in the Zikzov quarter, to see the national memorial and the beautiful view of the city. Petrin is also really nice. In the surroundings of Mala Strana, you could leave the busy main roads and walk around in other streets to avoid the mass and crowdedness of tourists.