On top of those suggestions listed above I would also make a backup to the computer, then attempt to sync to the computer. I've seen the sync process help those files that are "deleted" but still listed as using memory. If the sync doesn't help try a reset to factory setting and then restore from a backup.
Also, before you do all this, make sure you have all your contacts backed up as well as saving all your photos directly to the computer outside of the iTunes backup. Game high scores suck to lose as well as rambling iMessages between you and family/friends, but most people regret losing photos. And if you do have text messages you want to save there are apps out there that can extract those messages without having to jailbreak your device.
If the problem persists after a reset/restore it could be a corruption in the OS, which would also copy over into the backup.
If you have to start over add apps slowly, because sometimes apps can cause problems and you might be able to figure out which one it is. Facebook was notorious for a while for causing problems, as well as those slot games, and some of the kids games.