This is best handled in your backup software, if it's really that much of a problem (do you honestly have that many big duplicate files on your machine?) I know BackupPC purports to solve this problem by storing everything under the hash of it's contents and indexing from there, but whether that's compatible with your OS is unknown.
Finding dupes isn't hard -- just md5 hash every file on your system and anything with the same hash is a candidate for duplicate detection (still need to compare the actual file contents to make sure it's not a hash collision). 20 lines of shell script or Powershell should do it. But what are you going to do once you've found them? Deletion would work, if you only need one copy, but otherwise if you exclude them from the backup then the backup won't be complete. Far better to have the backup program deal with it for you.