Why don't the sizes of my folders add up to the size of my hard drive in Windows?

There are hidden files and directories which contain system files that are not included in the calculation. System volume information, for example, contains your system restore points and volume shadow copies among other things. It is not included in the calculation because by default the ACL does not allow your user account to view the folder or it's properties. You can gain access to it if you really want to, however.

On another note, the cleanmgr.exe utility (better known as Disk Cleanup) can help you reclaim most of your disk space. The More Options tab allows you to delete all but the most recent restore points and Volume Shadow Copies.

Use WinDirStat to see where your files are taking up space:

http://windirstat.info/

It is free, lightweight, and there is no easier way to see your usage by directory.

Here's a comprehensive list of all the reasons I can think of why the used space in a hard drive may be greater than the sum of the file sizes. OP has already solved his/her problem, but the issue may remain for some lurkers.

• A file takes up more space on the disk than merely its size. For example, a text file that contains the letters "hello" has a file size of 5 bytes, but it also takes up space in the filesystem's table to store its name and properties. Usually the difference is not greater than a few hundred bytes, but if you have many tiny files, that can add up to quite a bit. You can see the difference by comparing "Size" and "Size on disk" numbers after opening the properties dialog of a file in Windows' file explorer.
• You may be forgetting to check hidden files: make sure you have "show hidden files, folders and drives" enabled in Windows' file explorer options.
• You may be forgetting to check system files: make sure you have "hide protected operating system files" disabled.
• You may be forgetting to count the recycle bin which is a special case of hidden and system files.
• Contents indexing takes up space: if you open the properties dialog for a partition, you can see the option "Allow files on this drive to have contents indexed in addition to file properties". This takes up space, I'm not quite sure where on the file system.
• Previous versions (or shadow copies or file history) take up space: NTFS has the feature of shadow copies of files, which takes up space not counted in the plain file size.
• You may have enabled compression: this should theoretically cause the used disk space to be smaller than the sum of the file sizes, rather than bigger, but in any case, it's a spanner in the works. You can check by opening the properties dialog of a partition in Windows' file explorer.

Also, remember that you may have hidden partitions, or unallocated space on your hard disk where you could have a partition. Open "Disk Management" shipped with Windows to check this.

If anything is missing, go ahead and edit my answer to make this as comprehensive as possible. I'm happy to make this a community wiki post.