If it's only happening on HD intensive tasks it sounds like the HD controller (or the HD itself) is having problems. If you don't have Smarts turned on in bios turn it on so the HD can do and report full diagnostics. Run the HD manufacturer's diagnostic program (after smarts is turned on).
It could also be an IRQ assignment conflict. If you have an expansion cards installed swap slots. This will change the IRQ used.
It's been a long time (decades) since I looked at the wintel device level architecture but from what I recall Windows maps almost all the hardware devices down into just a couple hardware interupts (as opposed to a polling system) using software interrupt requests IRQs. The keyboard might have had a hardware interrupt and the watchdog timer.
The problem is all the devices eventually map into a "hardware interrupt" so anything could be misfiring and producing excessive requests for servicing. If you want to isolate it start pulling/disabling hardware one device at a time (sound, USB, CD/DVD, LAN, etc). It could be a MB problem too. An unterminated input on the interrupt controller could just be bouncing around causing false inteerupts. Something like a heavy disk access (rar, downloads, etc) could be causing higher noise levels and more false interrupts.
Isolate what you can and if nothing removes the problem then the MB is suspect.