I have an eMachines M5310 notebook which runs very hot whenever CPU instensive tasks are running and automatically shuts down. I was unable to complete a Spybot scan without having the notebook automatically shut down.
To resolve the problem, I installed SpeedSwitch and set the CPU speed to maximum battery. This lowered the maximum CPU speed which prevented the shutdown due to the CPU overheating.
The SpeedSwitch home page is at http://www.diefer.de/speedswitchxp/index.html.