I have this exact same issue on a Dell D620 Latitude. It typically happens when compiling code. The exact same symptoms - machine is working hard, begins to heat up, machine gets really slow and cools off but remains glacial slow. I've ran one of the speed / temp sensor plotting tools and can see the result CPU running at half speed but working at 100%. System is so slow that moving the mouse and the like around is practically impossible, only a hard reboot clears the machine, if I soft reboot the problem is even in the bios (pushing down arrow is about 1 second to move to next selection). The machine normally does ~6000 bogomips, when running slow is about 200 bogomips.
I have had the motherboard and cpu replaced multiple times (4? 5? something like that). It always reoccurs a couple of months after the repair. This issue isn't confined to my D620, but all my co-workers which receive the same model Dell laptop have also had significant issues. It is so bad that we will be replacing our machines a year before they would normally be replaced. I'm lobbying hard to get something other than a Dell, but this is a challenge as they are my companies primary supplier.
The most annoying thing, is when the problem happens and you call Dell up they are always - please reinstall the operating system. I know it isn't the operating system, I can reproduce it in the bios. But they still persist in believing it is the OS (and yes, they are trying to blame Microsoft, this case, purely Dell's problem).