I've stayed at a suite in City Hotel which, while not the most sophisticated property I've been to, had very friendly service, free internet, a great breakfast and charged less than EUR100 for the suite. Slightly outside the city centre- 20 mins walk or about 8 in a taxi (very cheap).
I see prices have gone up a bit (the Czech and Slovak crowns have been gaining against the Euro), but I'd still recommend it- just stay at a "business double" or some such.