You can disable all no-Windows things on the Startup tab without causing problems to gameplay, vice versa. Disabling your antivirus may have undesired effects, though. Fiddling with the other tabs might have more side-effects. On the Services tab hiding Microsofts services may help sorting out those that could affect gaming.
And really, without trying to be the annoying wiseguy, if your "yes" meant all those things I mentioned, it is most certain that there are open handles left from the applications they have used. Thus a reboot every now and then is not to be avoided. Heck, I seem to benefit from a reboot before AH even after letting my daughter spend her hour using Messenger and Deviant Art alongside of some web comics!
But, if I understand right, if you lose performance after a reboot during only playing AH, it sounds as if there really is something using your resources fast. If you checked for malware only in Windows, it could be possible that you have a rootkit or MBR virus which hide themselves very effectively. Download and run some Linux based antivirus program. I like
F-Secure's rescue CD, because they have quite a good rootkit finder. Running
ComboFix could also help in finding effectively hidden malware. And ProcessExplorer, which I recommended earlier, is of good help trying to find out what's running under the name svchost or any other service.