Depends what kind of thing you're looking for; if you want a full-fledged hotel with all thye trimmings, then there aren't many cheap ones left in Prague, and those that there are aren't terribly conveniently situated. If you're just after a good clean B&B with a simple but filling breakfast and the world's (well maybe not the world's, but certainly one of Europe's) cheapest minibar I'd recommend the Pension Dana Residence. It's in Strasnice, 10 mins walk from Skalka metro staion and 3 mins walk from the tram into the city centre (about 15-20 minutes). It's a quiet residential neighbourhood with 3 or 4 good and cheap restaurants within an easy walk. I've been going there several times a year for 6 or 7 years now and always found a warm welcome.