The Upload Directory Cleaner plugin allows you to scan and delete all unregistered files from your WordPress upload directory.
Prior to cleaning your upload directory, you can take a quick one-click backup of the directory, choose specific directories or file types to exclude, choose to retain existing thumbnails, and opt to remove empty directories. I've only done minimal testing, but it seemed to get the job done decently well. Use at your own risk and let me know how it goes.
