My C:\WINDOWS\Resources\Themes\ folder looks like this:
There's the Luna theme [default] and 2 other themes which I added. So if I wanted to clear it out, I'd just leave the Luna theme and folder.
I think Windows Classic is supposed to be there, so if that's there, leave that as well.
To do a cleanup, I use Disk Cleanup (Accessories > System Tools) which does the job well.