I like Orbitz. I've gotten a few "rate assurance" rebates from them. With airline and hotel prices changing day to day, it's good to have that as backup.
I've also had good luck calling pricey hotels directly. "I will be traveling to your city from date to date and would prefer to stay with you, but the rates aren't to my liking, is there anything you can do?" If they have more than a handful of unbooked rooms, they'll deal and will match almost anything out there. When a caller books directly, there's no commission, so the hotel can offer a very good rate and still make more than if you booked through an online site.