Unless you often need windows to rearrange programs on your hard drive (via scandisk), you can delete logwat95.exe (all instances on hard drive) and see some of the thrashing and slowdowns stop. That one watches how you use programs, logging most ofyour activity.
Another is findfast.exe (windows puts that in your startup folder) delete that shortcut, reboot and see much less unwanted HD activity. It defaults to a refresh about every 15 minutes and reads every directory on every drive.
Another slow-boot device is any office toolbar program you find in your startup folder.
if you use Lotus notes, you can delete QNC.exe and any instances of *.rip files on your HD. These are nothing but trouble.
If you are networked or dialed up when the HD thrashes, there could be some other things going on (from virus to net management programs). See if the same thing happens when not connected to anyone.