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The Windowsserver blog has an article on Windows Server 2003 Access-based Enumeration (ABE) and also details of Single Instance Storage (SIS) for Windows Storage Server R2. The ABE tool is well worth the read and a download, and if SIS can save you 60% of your storage space then that must be worth looking into as well. SIS is definitely on my "to do" list.
UPDATE: https://blogs.technet.com/filecab/archive/2006/01/23/417965.aspx some more ABE info that's just been posted