Removing apps from 'Mobile Applications' that aren't in iTunes?
I don't know of an effective solution.

One approach could be trying to process the iTunes Library metadata files to see if you can extract the raw filenames from that. There are some third party programs that read your iTunes Library. There's an one open source library called sift that does that.



In addition to this, I can think of a workaround requiring some work. Not sure if it will work for you:


Remove all apps from iTunes without deleting the files.
Re-add the complete folder.
Re-delete all the apps you don't want from iTunes, making sure you chose to delete them from disk as well.