Like Anchorhead, I'm popping out the "bonus" discs and putting them in my own cases -- you know the artwork is probably going to be the same crap as on the boxed versions anyway. Then the offending discs and packaging will be stored away out of sight just incase I ever need to sell the whole shebang for a future upgrade.
I just made some modifications to the artwork I had previously done for my LD versions; original movie poster art all personally scanned (no crappy low res JPEGs) including a REVENGE of The Jedi cover! And alternate poster art for the inserts. I just hope the discs themselves don't have crummy looking art printed on them.