We really liked our stay at the Hotel Color. It is a budget hotel, but it was clean and tidy and had good basic facilities for a comfortable stay. The bar was small, but good, and there was a restaurant that served breakfast and dinner, although we did not eat there.
We stayed for a week and had a hire car, and found that the hotel was an ideal base to visit Vienna (1 hour away), Budapest (2hrs) and Brno (1.5hrs). Bratislava itself was great, although you'd probably struggle to spend more than three days visiting its sites. Bratislava has great food by the way - try out the UFO restaurant, slightly pricey, but the view is worth it, and 1 Slovak Pub is great for authentic Slovak food and beer and was really cheap.
The only major negative we found was that the room did not have aircon. We had to leave the window open at night, but got bitten alive by the mosquitos that visited. We also found that the public computer either did not work or was really slow. Wifi for mobiles etc was really good though.