Okay, I posted earlier and really just wanted to watch this thread to see if anyone had any suggestions. I have not experienced this problem since the day I first posted. My iMac is on 24/7, I access it remotely from work using Back-To-My-Mac.
This is all I did.
1. Downloaded and installed a newer version of Flash. The problem seemed to happen to me when using the internet. Many sites have flash, and you don't even know it.
2. Shutdown iMac, then held down power button until I heard the long beep. This resets something, but I can't remember what it was right now, maybe SMC?.
3. Restarted iMac and pressed ctrl-option-P-R to reset PRAM. This will work even with my Apple Wireless Keyboard. (This was the first time I've reset PRAM in 2 years of ownership, at work PRAM is usually one of the first things I do when a user has problems).
I'm pretty sure that it is not a temperature related problem. At one point I even had inkscape/gimp/espresso/cssedit/chrome/iMovie/Keynote/Pages running, watching TV on hulu on my external monitor while doing some web work with movies on the main screen. The iMac was so hot even the room was warm.
BTW, I didn't install the Combo Update for 10.6.3... so It looks to me as if the 10.6.3 update was of no consequence.
Your Mileage May Vary