Have you considered a virus? That could be what is spinning your hard drive out of control, resulting in the overheating.

A couple of cheap and easy tips that I can share on keeping your system cool: 1) Take off the side panel case cover. Just leave it off. It does allow more dust into the case, but the increased airflow actually let's less dust just sit in the same spot, and keeps the system drastically cooler. 2) Get a desk fan and point it right into the case. What I actually did was take out the popout panels where you can install CD drives, and point the fan right at the holes. It looks ugly as sin, but the cooled air blows right at the hard drives, and with the side panel off, that now heated air blows right out the side. My computer is never too hot anymore, and I used to have a bad problem with heat. 3) You can buy a power supply with dual fans. One points down into the case, pulling the air into the power supply, the other blows out the back of the power supply. This is a decent solution to grab heat. It actually works really well on my computer, since the setup has the power supply right over the CPU, so the CPU fan blows the air up toward the suction of the power supply, and then it gets expelled from the case. Keeps the CPU very cool.

Heat is the 3rd worst enemy of computer equipment. Ahead of them on the list is static electricity, and power surges. (If you can afford an Uninteruptable Power Supply [UPS] that is a great investment to prevent things like lightning from causing unseen damage to your system. To combat static, always ground yourself before touching your equipment. (Touch an unpainted metal part of the outside of the case, or a doorknob.)