FileUniq identifies duplicatefiles, and optionally removes them or replaces them with hard or soft links. It is designed to work well with heavily hard-linked cp -al / rsync backups. For more information please see http://fileuniq.sourceforge.net
Cozy is a backup solution for Linux. It aims to be similar to Apple's Time Machine, with the difference that Cozy recognizes duplicatefiles and incremental backups are realized through binary diffs to save space.