You must try Dupe Checker Pro. I had the same problem. A lot of files, different filenames, but maybe some of them are dupes. Ooh my God, I thought, to sort them I will spend all my life :-)
And not a lot of time ago my good friend adviced me this application: Dupe Checker Pro.
I got fantastic result. This app can eluminate duplicates not only by filename, but by much more options: by filesize, file content (byte-by-byte), date and time and more and more... Then You can remove them or put to some folder.
So, download it on: http://www.atory.com/Dupe_Checker_PRO/ and don't waste Your time...