I should have further clarified that no one else has written anything that does close to everything that iTunes can do. Emplode was fine for moving files over the the empeg but that's about it.

Your use of iTunes seems a little cumbersome - it's not the way it's designed to be used. Seems like you'd be better off turning OFF automatic sync and just dragging whatever files you'd like to the iPod yourself. You're not using iTunes as a music manager but rather as a file loader.

I'm not sure about iPhoto, but in iTunes you can get "info" on any track and it will display the full path to the music file on the first tab of the resulting window.