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Commentaries:
Most episodes have 4 audio options. But as you watch Stark Raving Dad, Lisa's Pony, Bart the Lover, or Separate Vocations, you can get a 5th audio opinion: English 5, this is the second commentary.

Outtakes:
Put in disk three of the set and let it go to the main menu. When you get there, hit the numbers 84763 -which are the numbers that come up when maggie is scanned at the cash register. It took me a few times to do it right, but when done properly it takes you to a menu with a handfull of funny audio outtakes of some of the actors and guest stars adlibbing.
Reported by: Jabberwocky

Deleted Scene:
Go to the radio bart episode and press right twice left twice and then up three times you will see a 2 minute deleted scene from radio bart.
Reported by: MrHappyHamster

Bonus Feature:
On episodes Like Father Like Klown, Black Widower, and Homer Alone some sentences appear in the Simpsons yellow font. Press play or enter a few seconds before and you get to see sketches drawn by the animators of the scene.
Reported by: CarolynC7169Production Art:
Thirteen random drawings by the animators can be seen by entering 7, 4, 2 and pressing enter after each number on the remote in the "Special Features" menu of disc four.
Reported by: John Winchester