This is the first time urination is depicted in The Simpsons. An alien pees in the fountain before a security guard shows to stop him on which Homer was telling Bart about how guards are.
Edna Krabappel can be seen inside one of the tubes in the probe room of the spaceship.
Inside the ship, there might appear a picture of Kang and Kodos in a reference to the All your base are belong to us meme. Also, both aliens are dressed exactly like the game character who said the phrase.
In the PS2, Wii and PSP games, there is no Space Invader reference and aliens continue to spawn after you have destroyed all the buttons in the space ship.
In the Xbox and PS3 games, after Homer and Bart enter the Kwik-E-Mart they fight three waves of aliens, similar to Space Invaders.
In the DS game, only Bart is playable, the entire level, save the Space Invader reference, is omitted and he cannot move around the area freely, only using his Slingshot to defeat them.
The rakes aren't visible until Sideshow Bob and Kang step on them.