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Interface:
Disc 1: If you have the very first episode highlighted, and hit up, a phonograph looking thingy is highlighted, and pushing enter will cause it to play some obnoxious tunes.

Interface:
Disc 1: If you hit up, and highlight the phonography thingy and hit right instead of hitting enter, a lever will be highlighted, which will cause an alarm to go off if pushed.

Clip:
Disc 2: highlight the first episode, then hit up. A portable TV on Bart's bed will light up, and will play small clip from Itchy and Scratchy.

Interface:
Disc 2: Hit right while the portable TV is lit up instead of hitting enter, and a Casino sign will light up. It will turn on if you press your Enter button.

Interface:
Disc 3: Highlight the first episode and hit up. This highlights a Malibu Stacey doll on Apu's counter, which will talk if you press your Enter button.

Interface:
Disc 4: Hit up and highlight a box on Ms. Krabappel's desk and press your Enter button.

Interface:
Disc 4: Also hit right on the arrow after the box is highlighted to highlight a plant in the corner that is shaped in Marge's likeness.

Commentary:
On Disc 4, on the "Art and Animations" menu, you can highlight the 100 episode banner to hear a secret commentary on the animatic. (Can also be accessed by using the 'Audio' button on the animatic.)
Reported by: John Winchester