I stayed at the Hotel Matelote, Haarstraat 11a, which was extremely convenient to walking the entire city. It is a boutique hotel that has a very contemporary style in an older building from the 16th century. I loved Room 7 on the second floor which was large and bright. The staff was very helpful particularly when it came to restaurant reservations and special requests. They have WiFi and breakfast in the dining room off the lobby.
Another great choice is the Hotel Julien located on Korte Nieuwstraat 24, a short distance from the Cathedral. This is a small boutique hotel with great style.
The CMB58, where you stay on the first or third floor in a beautifully decorated townhouse, comes highly recommended by Wallpaper* Magazine.