Although you didn't say which OS you're running, if it's Vista/7 I would venture a guess at it being ReadyBoost/Superfetch. That bothered me so much that I turned it off. I saw negligible improvements for loading programs with it on, and all it did was spin my HDDs; reducing their life to pre-load programs that I may not even be using that day. I'm very sporadic with my usage on certain programs.
If not the above, then you may be infected with McCrappie and/or mirAgent. In which case you should probably light your computer on fire, then throw it in the nearest active volcano just to be certain the problem is properly dealt with. Don't worry about the travel costs to do so, or the loss in hardware/data/software licensing/time invested...it will be time & money well spent.
Do what BFG10K said (unless you're pre-Vista, then you'll need a 3rd party program to monitor that activity). You can try deciphering it via I/O activity columns under processes but that'll likely get you nowhere definitive.