I've had a GTX 660 for about two months now, and I've been quite pleased with it.
For the last 24 hours, however, it's been unstable (display divers stop working, games are very choppy even when nothing is going on) and running at 65-67 degrees Celsius while idle - quite a bit more than the 30 or so it was running at before when idle.
I've checked the fans both physically and via software, and they seem to be working just fine. I've uninstalled and reinstalled the latest NVIDIA drivers, and even given the beta drivers a try. No dice so far.
I have been battling a malware/virus infection for about the same amount of time... is it possible that they're connected?
If you can remove the card and double check the cooler is mounted properly to the card. Try removing the shroud to check it (you won't void warranty). It sounds like the cooler is not sitting flush with the components, its possible a clip has come loose or ever broken.