For managing fragmentation of NTFS (Windows Server 2003/2008, XP, Vista, and Windows 7) : For general disk defragmentation, the following utilities offer a substantial improvement in overall performance and efficacy over native operating system tools: Auslogics Disk Defrag or Raxco PerfectDisk For use on disks unsupported by the above tools, frequently executed and/or locked files or even a straightforward command line utility that can easily be used as part of a shell script: Contig from the Sysinternals Suite Contig has been of particular value when managing backup servers - servers storing huge files with substantial writes on a regular basis. Being able to specify the backup files allows for properly scheduling defragmentation by backup job, and in the process eliminating the need for downtime on these systems as part of this manner of disk maintenance. Can also be used for per-file fragmentation analysis and reporting. For managing fragmentation of ext4 file systems ...