I am wondering if this is your situation.  An application is created for the use of an individual, and, after that person leaves, the application is no longer needed?  If so, I am thinking the solution would be to maintain a database or spreadsheet showing which applications are personal, and will not be used by their successor.  A similar situation exists for a unit that has an application created for them, but the unit is disbanded, and the application is now ownerless.

Activity Trends under Databases > Inventory has a column for "Last Active."  I believe this means the last time a document was added to the application.  An application that was used for a past project would not have new documents added to it, and so would show in Last Active column with a date from some previous year.  The Last Active Column is sortable.

Another thing to look at is the Admin process.

As part of the user delete, an Admin task to delete the user's mail file usually gets submitted, but need to be OK'd by an administrator.

So if no-one is watching the Administrative Requests database, the requests will just stack up.

Open the admin4.nsf database, and check the 'Pending Administrator Approval/Pending by Server' view for 'Approve Mail File Deletion' requests.

This won't help identify files that aren't getting used, but will help clean up databases that are already tagged to be deleted.