Hi Steve,
Clean up of files is best done manually IMO.
Little bit of a PITA, but I don't want an app deciding which files get deleted.
As far as cleaning the registry, if you do a lot of install/uninstall, it's a good idea to clean out the registry.
Many apps leave lots of "remnants" in the registry when uninstalled.
Ccleaner is fine for this purpose...
Always make sure you have an up-to-date backup image (when the system is working well)... and you're good-to-go.