I had some good feedback on my last post, that it would be useful to be leave just the superfluous duplicate files marked in the dired buffer. After doing that you can then copy them to another folder, or delete them.
I've added a function to do this `dired-mark-duplicate-files', and updated the google code site with the changes.
To copy to another folder use R and select a folder to move the dupes to. In order to delete them hit D.
Tags: emacs md5 duplicate files dired