Check your logs (dmesg, syslog and messages) for possible indications on why this happens.
If you suspect high temperature as the main culprit, there are applets to monitor temperatures of different parts of the system. Install it.
Also, have you tried to do a Ctrl-F3 (to go to the console) when Gnome becomes unresponsive? Or if you have another computer on the same network segment, try to ssh to your computer and see what is going on (dmesg, the logs etc.)