Free Disk Defragmenter
UltraDefrag
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Good Open source defragger - http://ultradefrag.sourceforge.net/
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Tends to peg the CPU, especially at initial scan time. Consider start w/low priority and non-"all" CPU affinity.
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Portable Apps has a distribution. At time of writing, the regular SourceForge download is blacklisted by Google Chrome
Others:
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A great, free windows defragmenter - http://www.dirms.com/ - it's sister program runs nicely in the background. It certainly seems to do a much better job than the defrag included in WinXP. Warning: I have had it hang the computer before.
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contig from SysInternals. By concentrating it's efforts on a single file, you can defrag what is most important to you (like a 4GB database file with 17000 fragments :)
"contig -s *" will recurse through the folder, one file at a time.
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Note: contig does NOT consolidate free space, so fragments can, in some situations, come back quickly.
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Also: contig runs with user permissions, so if you do not have permissions to a file, you can't defrag it, you can run it with Local System permissions w/ "psexec -i -s cmd.exe" (also from Systernals)
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contig will run via psexec
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Another freebie: http://www.geocities.com/andreigaceff/indepth_DefragNT.html
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The fellow behind contig.exe also kindly put some documentation to NT's Defrag API online. See "Sysinternals Freeware - Inside Windows NT Disk Defragmenting" at: http://www.sysinternals.com/Information/DiskDefragmenting.html
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Another promising freebie defragment tool. It can defrag NTFS metadata with a boot-time defrag.
http://www.whitneyfamily.org/Hacks/?item=Defrag
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A little vbs script to use windows 2000's built-in defragmenter in a scheduled task.
http://www.compu-docs.com/W2KDfrag.htm
Windows Built-In
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Vista's defrag has some hidden command line options:
http://www.nerdgrind.com/disk-defragment-windows-vista-from-the-command-line/
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Win7 (maybe earlier?) has /x option to consolidate free space - handy to do this if a disk got ridiculously fragged, this will prevent the next file from using the higly fragmented free space.
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Tags: defrag, defragment, disk, optimize