I have this problem, I've found it's music/videos that you have removed from your phone, where the file is removed from the library, but not from the phone.
the only fix I've found so far, is to turn off music/podcast/film/tv show etc syncing. Sync to remove all your media.
then download and run iPhone explorer (does not require jailbreak), go to the media/itunes folder and delete the mp3's/video's (which shouldn't be there as you just un-sync'd them!) While doing this you'll see "other" shrink in iTunes, down to about 0.4 gig.
repeat every month or so, hope they fix this bug soon!
(it's not files sync'd to applications like VLC, that all goes under "apps)