The Scandic Front is my favourite in the Nyhavn area. If budget it tight, there's also a Wakeup hotel in this part of town - tiny rooms, but a solid, modern hotel.
Near the station, Tivoli and Kødbyen, I like the Andersen Hotel, but it's right in the red light district, and pretty in your face at night. Some great places to eat nearby, though.
Up the other side of Rådhuspladsen is the new and decent, if overhyped, new Sp34 hotel, where I stayed recently. Also a good area to be based in, and handy for Vesterport station. Like the Andersen, it's a traditional round-a-courtyard style hotel that's been nicely refurbished.