The defragmenter in Windows 2000 & XP is a stripped down version of Diskeeper, a software written by Diskeeper Corporation.
The CEO of Diskeeper is a scientologist, and he has stated that his employees are schooled in the principles of Scientology and that "I attribute [our] success directly to the management technology developed by L. Ron Hubbard. Simply put, I couldn't have done it without his help."
Diskeeper Corporation denied tech support to Ciba-Geigy, the company that makes Ritalin, because scientology opposes psychiatry.
The German government demanded that Microsoft release the source code for the defragmenter before using Windows 2000 on their computers. Microsoft resolved the issue by not releasing their source code, but rather releasing a utility to remove Diskeeper.
Since neither Diskeeper nor Microsoft are going to release their source code, it's impossible to know exactly what their software is doing to your computer.
I don't know if the Vista defragmenter is based on Diskeeper, but either way, it's a crappy defragmenter.
Ironically Diskeeper is one of the best defragmenters out there.
http://en.wikipedia.org/wiki/Diskeeper_Corporation#Scientology_and_Diskeeper
http://en.wikipedia.org/wiki/Diskeeper#Controversy
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