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.