There are three schools of thought here:
Somewhat limited as systems are different and they are normally a bit like virus checkers in that they check against a database. I would not trust any heuristics here as a false positive on a virus is able to be dealt with but a messed up service/registry entry is a bit more complex. Alas I do not use them so no links from me.
DIY (including guides)
Here you find the services, drivers, registry additions, files and whatnot and erase them. Hard to do and in my opinion at best a stopgap measure http://www.tweakguides.com/ is a nice start.
Easiest (take a look at the many windows tweaking threads around here), my favourite is to create a custom disc with nlite ( http://www.nliteos.com/ ) and then maybe image the drive once all is said and done.