If you are seeing a continual slow down on boot up, my guess is that it is a recent program you loaded or a combination of virsus and trojans. They always kill performance. A quick way to check for the most current ones is MS's free tool:
http://www.microsoft.com/downloads/details.aspx?FamilyID=ad724ae0-e72d-4f54-9ab3-75b8eb148356&displaylang=en
Like Joe said, a FDISK / reformat and reload is always a good idea, especially if you are still running Windows 98. This is the only way to be sure you have a clean system and improve performance. BTW, the new generation of 7,200 RPM hard drives might be the best way to improve performance short of a motherboard transplant I have seen. My new 80 Gb drive in a Dell Latitude D400 is clearly faster in bootup, shutdown and most importantly application useage.