Starting in Windows Vista, the construction of the Windows directory causes system tools to report that it takes up more space than it actually does. Specifically, it's the WinSxS directory in the main Windows directory that is the "problem."
The WinSxS directory is almost completely populated by what are known as "hard links." Think of a file as a specific location on the hard drive's physical surface. Each file has one or more entries in the Master File Table. The MFT is basically the Table Of Contents for the hard drive. When anyone opens a file, Windows uses the MFT to find the specific location on the hard drive to find the file. Each actual file on the hard drive, however, can have any number of entries in the MFT, each with a different name and possibly other directories. The WinSxS directory uses this feature to have a central location where all the important files in Windows exist without actually making a copy of the files on the physical hard drive. This space-saving technique ironically makes it seem that Windows is using significantly more space on the drive than it actually does.