doporucujem vsetkym precitat si o tejto problematike na wikipedii:
http://en.wikipedia.org/wiki/File_system_fragmentation

pre tych ktorym sa nechce citat vyberam odstavce, ktore tu uz boli nacrtnute a tiez dolezite veci ktore tu chybaju:

A relatively recent technique is delayed allocation in XFS and ZFS; the same technique is also called allocate-on-flush in reiser4 and ext4. This means that when the file system is being written to, file system blocks are reserved, but the locations of specific files are not laid down yet. Later, when the file system is forced to flush changes as a result of memory pressure or a transaction commit, the allocator will have much better knowledge of the files' characteristics. Most file systems with this approach try to flush files in a single directory contiguously. Assuming that multiple reads from a single directory are common, locality of reference is improved. Reiser4 also orders the layout of files according to the directory hash table, so that when files are being accessed in the natural file system order (as dictated by readdir), they are always read sequentially.

The HFS Plus file system transparently defragments files that are less than 20 MiB in size and are broken into 8 or more fragments, when the file is being opened.

Amiga SFS (Smart File System) defragments itself while the filesystem is in use. The defragmentation process is almost completely stateless (apart from the location it is working on), which means it can be stopped and started instantly. During defragmentation, data integrity is ensured for both meta data and normal data.