After my clean install, I installed Advanced Windows care and Ccleaner. I ran them in that order, with the defaults. They did no harm, that I could see, to my setup. They did, however, remove a lot of entries from regedit. Many of these, if you examine them, are there from previous OS's, and ,I hope, AWC detected them as such. I then installed the whole of my software and configured it, and ran the two programs again. No probems. Maybe I am trying to imagine something which is not hapening, but in Vista and 7, I am certain I noticed an improvement in performance.
I was reading one a comment by a Microsoft administrator I think who said you really don't need to tinker with the registry especially windows 7. Keys are supposed to be different than the other os,s and most companies wouldn't know how to deal with it anyway.