Why Does Windows Bog Down?

It never fails. Win 9x, Me, XP Pro after running for a while start to bog down and get slower. A format & install, even reinstalling the same programs always results in a much faster system. Why is this? Is there a utility that will REALLY “clean up” Windows so I don’t have to format? I have looked at Registry Mechanic and don’t mind spending the $ if it really will work. By running NAV, Spybot, and Adaware, I am reasonably sure it is not an adware/malware/virus problem.