Awhile ago I found this interesting defragmentation program for Windows. It is called Diskeeper 2008 and has a 30 day free trial. I put it to use and I have to express how completely impressed I was and still am. You can enable a process that runs in the background tapping unused resources to keep your system defragmented at all times, and help to keep files in one piece as you put them on your computer. Not only that, but running defragmentation manually is extremely superior to the default windows defragmenter, and is created by the same people! I have seriously enjoyed the trial and typically run defragmentation multiple times in a row to eliminate fragments of problem files that don't necessarily go the first time. It also has boot-defragmentation for places it cannot usually defragment while the operating system is running.
This program DOES cost money once the trial is up, but I find it to be worth it for the sake of computer performance and organization.
There are various editions of the software which can be useful for various things, and you may choose to download and use the trial for the one that you prefer. I personally went with the home pro premier edition, as it seems to be the best in it's class for personal use.
http://www.diskeeper.com/diskeeper/diskeeper.asp
