For sound files to appear in iTunes they have to be actively added to iTunes. itunes does not go out and search for all sound files. Did you do something like drag your hard drive to iTunes, or run an iTunes script that might have caused it to search a drive for all sound files?
Right click or use iTunes File command to reveal the file. It is one that has been added to your iTunes folder or is it still in a system folder somewhere?
iTunes was created to be the sole music player for Macs. If you clicked on a folder or song file and it opens in iTunes, it could be saved in your library. The best way that I can think of is going through and holding down the CMD button and click the song clips you don't want. Right click and select sent to trash.
Be careful about sending to the trash. Depending upon your iTunes preference settings you could be sending the actual system file to the trash which could mess with your computer. This is why I suggested revealing the actual file used by iTunes to double check it was a copy placed in the iTunes folder, not the original.
Thanks for the suggestions and help. While the cause of this problem is still obscure, we've managed, with an Apple tech's help, to remove the system/application sound files from both the iPhone and iTunes. We used Time Machine to backtrack to the point at which the sound files first appeared in the iTunes folder, then moved back one more day and restored the iTunes Media folder (where all the music was stored) and 2 iTunes files: iTunes Library.itl and iTunes Music Library.xml (we could also have simply restored the entire iTunes folder with the same effect). Then we synced the iPhone.
As for the cause, that's still a puzzle. From Time Machine, we were able to determine that the files were added between midnight and 12:47 AM on a particular day, but that computer was not in use at that time (the user was asleep in bed, and the only other person in the house at the time was me -- and I don't touch that computer).