When Bart first gets the grappling hook and uses it, he will sometimes say he is like "Spider-Man in a Batman costume".
The boss at the end of the level is Nintendo character Donkey Kong (or maybe his grandfather, Cranky Kong, based on first appearance and game).
The door opening and closing sound from Doom can be heard in the second room.
Somewhere in The Blood Room there is a graffiti saying The BFG, possibly a reference to the BFG 9000 weapon in Doom.
Also in the blood room, there is a large vat with "Achtung! Blut!" (Attention! Blood!) on the side spewing green blood. This is a reference to Germany's often strict video game rating system.
There is also Fatality graffiti on the walls, used in Mortal Kombat games when the player successfully completes a finishing move called a Fatality.
The witch laughter from Worms hell theme plays near the blood meters.
Donkey Kong forming a thumbs up while sinking into the green liquid bears a heavily resemblance to the T-800's death in Terminator 2: Judgment Day.
There are many posters of game publishers EA in this level.
All of the portal pipes are a reference to the Warp Pipes in the Mario games. In fact, the sound that Bart and Lisa make when going down one of these pipes is the same as the sound that is heard when Mario goes down a Warp Pipe.
The enemy football players can be heard chanting "4, 8, 15, 16, 23, 42, HIKE!", a reference to "the numbers" in the TV show LOST.
Homer's outfit is a reference to the character Link from The Legend of Zelda.
Marge's outfit is a reference to Princess Zelda from The Legend of Zelda.
The chests which contain different items are references to MMORPGs, along with fantasy games such as The Legend of Zelda.
Homer refers to Marge as being "a sexy MILF", which Marge corrects by saying that the word is "elf".
The Mobbits are parodies of the Hobbits from The Lord of the Rings. Marge will sometimes refer to them as "hairy toddlers", a sort of pun on the fantasy character name Harry Potter from the titular book series.
One of the Mobbits sometimes says that he prefers Narnia, the fictional land of the C.S. LewisThe Chronicles Of Narnia book series. It's either the Rod or Todd Flanders Mobbit that says this, since C.S. Lewis is a Christian book author.
Some of the characters and their costumes are from Earthland Realms, an online game in the Simpsons universe which parodies online MMORPGs.
Upon entering the maze area, Marge notices the camera switching to overhead POV (point-of-view). Homer states that this is just like his favorite old sword-and-sorcery game, Dig Dug - which is neither a sword-and-sorcery game nor even set in overhead POV, at least not until the sequel, Dig Dug II.
He possibly meant The Tower of Druaga, a fantasy adventure game also made by Namco, or more likely Gauntlet by Atari Games, due to the similarity of how its "narrator" points out things like not shooting the food.
In the background, people can be heard yelling "We shall surrender like we've never surrendered before!" and "I have surrendered, therefore I am!". They are presumably Cheese-eating surrender monkeys.
The Castle is named Castle Duffenstein, an obvious reference to Wolfenstein 3D.
Upon entering the church, Homer will sometimes say that he prefers "Castle Smurfenstein", possibly a reference to the computer game Castle Wolfenstein. The interior of the church resembles the decor of Wolfenstein 3D, an FPS predecessor of Doom.
The trophy Bart collects in this level is the movie "Saving Krusty's Privates", a parody of Saving Private Ryan.
One of the lines said by Comic Book Guy fire sumos is "Just a flesh wound", a recycled line from Final Fantasy IX which is, in itself, a reference to the film Monty Python and the Holy Grail. The line is indicated as such with Comic Book Guy laughing at the fact that he is taking it from Final Fantasy IX and not Monty Python and the Holy Grail.
The fire sumos make a reference to Cyndaquil, the Fire-type starter Pokémon from the Johto region.
The floating head talks to Homer and Lisa about the evil Rin Sha corporation this is probably a reference to the Shin-ra Company of Final Fantasy VII.
Defeated fire sumos sometimes say "Every light must fade, every heart returns to darkness", a line stated by Ansem from Kingdom Hearts.
Upon noticing Matt's piles of money, Bart says that the creator is "like Richie Rich, except straight".
In order to open Matt Groening's mansion door, the player has to do a Simon-type memory game, using floor pads that each play a different note. The song successfully pieced together is none other than The Simpsons Theme, which plays as the door opens.
Homer can say that he has an urge to sit on a couch, or has an urge to send money to Danny Elfman, who composed the Simpsons theme.
Upon entering Matt's office, Comic Book Guy points out the Evil Genius cliche as being "a rip-off of Lex Luthor," a constant adversary of Superman.
Matt introduces himself to the Simpsons by saying that "Your creator is TV's most beloved animation visionary!". Homer replies with "Seth MacFarlane!?"; Seth is the creator of rival cartoon sitcom Family Guy. During the battle between Bart, Homer and the many clones of Bender and Zoidberg, Matt sometimes says that he wished he invented Family Guy.
Matt's mansion has Futurama-like transportation tubes running along the ceiling.
While creating these "warriors of the future" Matt says "Say hello to my little friends!", a famous line from Scarface.
Insults thrown at the pair include "You were just too weird for network television!" (referring to Futurama's cancellation) and "You're my least favorite Billy West character!".
During the level's opening cutscene, all five members of the Simpson family are seen walking up the drive. When the gameplay starts, only Bart and Homer are present. Marge and Lisa reappear after that fight with Matt Groening, but Maggie doesn't.
The 'Video Game Engine Self-Destruct Button' is concealed behind a painting of Marge in the likeness of the Mona Lisa.
Another painting (seen only in the gameplay) resembles The Scream with Homer in it, and two statues resemble a Patty and Selma version of the Venus de Milo.
The trophy Bart collects in this level is the movie "Krusty Klownface", another reference to the movie Scarface.
In the DS version, at one point Bart jumps on notepads with the Simpson Family's Tracey Ullman Shorts designs.
This level has the most fourth wall breaks.
Matt Groening's secretary pronounces his name wrong and says "Groaning" instead of "Greyning", but he says he is not sure how his name is pronounced. This was also brought up in My Big Fat Geek Wedding.
The fact that Lisa uses her Hand of Buddha to build a tower to Heaven may be referencing the Bibical story of the Tower of Babel.
William Shakespeare is guarding the gates of Heaven. Bart complains about his "John Grisham fancy talk". The music that plays during his boss fight is "Anvil Chorus", a composition by Giuseppe Verdi, from the opera "Il Trovatore", also by Verdi.
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 has hundreds of hours of gameplay.