FSlint without hesitation, it makes a 3 verification of any file, with MD5SUM and other two signatures that I doesn't remember and shows you all duplicates even with different names.
You find it at Elive Synaptic tool.
The problem is that if you have a lot of files it take several hours to analyse them and it has no persistence, if you reboot you must analyse again.
The other problem is that you can automatically clean duplicate files with some criteria but until you are very familiarized with FSlint I suggested you to manually delete your files that will take you a lot of time, but its safer.
I goes slow, and every week I run FSlint to clean my tons of duplicate files. It will take me several months but I have less risk to delete accidentally files that I want to keep (some files I want to have them duplicates in several folders, and FSlint in automatised detection will delete all except one, so I prefer do it manually)
Try it, it's an amazing tool. FSlint + Unison is the best way to store your files as best as possible, since I discovered both my life has changed.