Disk Defragmenter does exactly as it seems - defrags your disk. Your disk being your hard disk drive.
When you uninstall a program, spaces (fragments) are left where the program was originally. These spaces are then left there to be overwritten by new data or simply left to stay (until you defrag).
Click on the picture to view larger. (It is obviously too small.)
You can see the little spaces in the picture above. This drive had disk defragmenter recently run, so there aren't too many fragmented files.
When you defrag your system, you are moving these spaces to the end of the "file" ("files" being where the old data once was) and moving the data currently on the drive together to create a continuous cluster of files.
These files are then read faster when you want to access them because there are no spaces on the drive taking up useless room.
[You should actually look at your own drive's fragmented files (you can access it by going to Start, All Programs, Accessories, System Tools, Disk Defragmenter) so you can tell what I'm talking about. There are numerous amounts of spaces (blocks) that represent certain characteristics of the drive. There is a little color map denoting colored boxes to their corresponding information.]
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