I belong to the kind of people who actually backup their computer(s), so I find that as I collect files I tend to wind up with multiple hard drives connected to my computer or networked (NFS) file systems with files and folders all over that contain redundant data.
First let me recommend CrashPlan, it’s a really good distributed backup system by the way, for multiple platforms. Free if you use distributed mode, optional you can buy cloud storage.
Then, I found a really good program called dupeGuru which takes care of solving multiple redundant files. And it is free, and for multiple platforms too.