Have you tried defragmenting your hard drive? Checking it for errors? Have you tried reinstalling windows? I'd also double check the drive's SMART status, failing drives have a habit of running hideously slow before they eventually die.
well, how much free HDD space do you have left? what cpu and ram do you have? it could be a number of things at this point until we have some details to go on, it could even be a virus, but sounds like a failing hdd like said above, it happened to me once