The space on your hard disk is not all taken up by user data files.
Just to begin, the system cannot index single bytes - it groups them in chunks called clusters. For performance reasons a cluster should be aligned to disk sector boundary (it was easier when said sectors were 512 bytes, before WD and large-size sectors), and a multiple of the disk sector length. Some prefer an integer power of two of the sector length, so 2 sectors, 4, 8, 16, or even 32.
Let's say that your NTFS system has clusters of 4Kbytes. This means that no file can occupy less than one cluster, and therefore a 1K file occupies 4Kb of disk. You can see this by asking for file properties: it will give you the file size, and the file size on disk, which is usually larger. There are techniques to avoid small files to suck up an inordinate quantity of disk space, but as a rule, for each file on the disk you lose half a cluster. So if you have 500,000 files and 8K clusters, that's two gigabytes lost just then and there.
Then, the system has to keep track of files - their owners, their permissions, their metadata, any alternate data streams, the lot. All this also takes space in the so-called Master File Table. There are techniques - lengthy techniques - to shrink and compact the MFT on a disk, better than what is done by Windows File Defragmenter, which may recover several gigabytes.
Finally, it could have happened that you did not actually select all your files, but left out some hidden and system files, many of them useless. The problem lies in sifting the dross: I once deleted a "useless" MSI file, and Microsoft Office stopped working.
A disk area that often gets overlooked is the System Recovery. The System Volume Information directory, if selected, could tell you "zero files and zero directories" -- but that's not true. If you gain access, you will see it holds lots of files. You might have a couple dozen recovery points for the last month; but if your system had no troubles in that period, you can usually safely delete all but, say, the last week.
A nifty utility that can get you many gigabytes and usually no troubles at all (unless you've got a really really dirtied-up system) is Piriform's CCleaner. It also has a "registry cleaner" function that is sometimes really useful, and a selective Recovery Deletion that's much better than the bundled utility.