I moved the so-called 'bonus' discs to the front and the SE rubbish to the back. I will soon be putting the cases into my 2004 box, and taking the other SE's from there out and giving them to a friend, who doesn't mind the changes so much. I thought of trying to sell them on Ebay, but that process is irritating, and this way my friend gets to own the films too, in a form I'm sure he'll be okay with.
Maybe I'll burn him some copies of the originals too, if he has any interest in them.