How to check which files are not in iTunes library, but are in iTunes folder?
You could move the location of your iTunes Media folder, which will only move those files actually in the iTunes library.

It may take a while, even if the source and destination are both on the same drive (it's still got to tell the OS to move each file individually), but should leave behind any files that aren't in the library.

The iTunes Media folder location is set in iTunes Preferences, under the Advanced tab. This will of course only work if you have "Keep iTunes Media folder organized" checked (which judging by your question is the case).

I would suggest something as simple as changing just the name of the folder it's currently set to (i.e. keep it somewhere in your home folder, or whatever drive it's currently on), and then move it back after you've cleaned out the 'orphaned' files.