When God is pleading Bart not to destroy his save games (on the ∞Mb memory card), he pleads "I'm on the final boss fight of Oblivion, I can't start again from the beginning!". The Elder Scrolls IV: Oblivion does not have any boss fights, rather, Martin Septim transforms into a dragon and defeats Dagon.
In the PS3/Xbox 360 version, the giant gold controller at the arcade game house is an "Atari" controller and when its button is pressed, four collectibles (Homer's Duff bottle cap, Bart's Krusty Koupon, Lisa's Malibu Stacy seal and Marge's Try-N-Save discount coupon) come out.
In the whole level Bart and Lisa (Homer for Shakespeare fight) are the only players in the PS2 and Wii version, while the entire family is played in the Xbox version.
The "Hii" (Xbox 360 version) and the "I Am" (PS2 version) are parodies of the "Wii".
Lisa seems confused why the aliens are in Heaven, when they possibly have their own. A similar joke was made at the end of The Simpsons: Hit and Run when Kodos asks why they went to Earth Heaven when they died.