Ninja File Managers - Suggest a killer file organization app.

[DimViesel]

Hey all,
File managers.
I am certain I have been on a page offering such an app. for download but passed it up at the time since it was not relevant then ( I am certain this is not uncommon ).
However I am looking for an app/tool that would allow me to build a list of files to compare (@ binary level for applications etc. & text for docs), the results would allow me to make a decision on reduandant 'repeats'.
I would then like to use this resulting info to record the versions of the selected remaining files & their locations. A linear list of this info would suffice.

The hope here would be that:

O this would reduce the redundancy in documents, apps & utils (resources) & allow to simply the maintenance process.

It was suggested to me that some kind of file manager, file organiser (organizer) would perhaps solve this issue.
Note that it is particulary important that I can automate the comparison process. Manually going through 4000+ potential matches would be time consuming.

Asking alot, but then computers were desinged to deliver in these kind of situations - perhaps you do something similar with a set of tools ?

Thanks.