Many times, its in the windows side by side assemblies. My c:\windows folder is showing 18GB used, when its really about half that. (Just got a new computer, old one showed over 30GB) If that is where the space is used, it is not actually using that much, it is the way that windows counts the hard links that the files use.
Hard links are used to point to the same file many different times, instead of actually hosting the file: IE, have one copy of a DLL, and then 5 other spots where it points to the same DLL. (but just points to it). That way, they can easily point to different versions of DLL's without the wasted space of storing them all. The way windows counts disk space used, it would count all 6 instances of the DLL. I have seen where the windows folder takes up over 80% of the drive space when you look at it, yet only 50% of the drive is used.