An even fatter Homer (who looks like Homer when he gained weight to get out of going to work at the nuclear plant in "King-Size Homer")
Animals on the island
Homer - Walrus
Marge - Panther
Bart - Spider
Lisa - Bird (Either an Eagle or an Owl possibly)
Maggie - Anteater
Mr. Burns - Fox
Mr. Smithers - Flamingo
Principal Seymour Skinner and Mrs. Agnes Skinner - Kangaroo and Joey
McCallister - Crocodile
Krusty - Lion
Moe - Toad/Frog
Cletus - Sloth
Chief Wiggum and Sarah Wiggum - Pigs
Nelson - Wolf
Otto - Camel
Professor Frink - Turkey
Mayor Quimby - Panda Bear
Manjula - Antelope/Deer
Reverend Lovejoy - Coyote
Snake - Skunk
Kent Brockman - Rhino
Selma - Elephant
Patty - Mountain Lion
Jasper - Goat
Grampa - Rooster
Dr. Nick - Squirrel
Sideshow Mel - Lemur
Judge Snyder - Hippo
Squeaky Voiced Teen - Donkey
Hans Moleman - Turtle
Comic Book Guy - Ram
Martin - Sheep
Groundskeeper Willie - Orangutan
Rich Texan - Buffalo
Mrs. Krabappel - Cheetah
Disco Stu - Shrew
Eddie - Dog
Lou - Cheetah
Ned Flanders - Cow
Wolfcastle - Jackrabbit
Apu and his octuplets - Possums
Gary Chalmers - Bear
Luigi - Guinea Pig
Various Springfielders - Monkeys (at the end when all the characters are in the pool)
This is the third and final Treehouse of Horror episode that does not have the credits littered with "scary names" (the previous two were I and XII, the first one was because the specials were just starting, and the twelfth one was because the writers felt that putting in scary names due to the 9/11 attacks was way too tasteless). This may have prompted some complaints from longtime fans, as the scary names were reinstated the following year.
This is also the last episode so far where each segment has a different writer.
The Island of Dr. Hibbert is a parody of The Island of Dr. Moreau.
As a bird, Lisa is no longer a vegetarian.
A deleted scene features Homer (as a walrus) giving Marge (as a panther) a back scratch coughs up a hair ball and Dr. Hibbert plans on changing the whole animals back into humans.
In the second segment, when the first Homer goes to the past, we would have seen Homer already since the future is not altered until somebody from the future goes back and alters it.
The War Room in this episode is very similar to the one seen in the Stanley Kubrick film Dr. Strangelove and one of the people in the room looks like George C. Scott, who played General Buck Turgidson in the film.
The music playing in the scene where Homer has been transformed into a walrus is reminiscent of the theme music from Fantasy Island.
Dr. Hibbert's lab is called the "House of Pain", the same as Moreau's lab in the 1977 film adaption of The Island of Dr. Moreau.
Bart, as a spider, spells out the phrase "Eat my shorts!" in his spider web from the 1973 and 2006 films of Charlotte's Web.
The first segment, "Send in the Clones," is a reference to the song "Send in the Clowns" from "A Little Night Music".
Peter Griffin from Family Guy is seen standing in a field full of Homer Simpson's clones.
A clone clones itself, resulting in significantly lowered intelligence from Multiplicity.
Homer travels back in time to save the future just like the Terminator in this movie. Then another future Homer comes from the future to save the Earth from destruction again just like the man from the film The Terminator.
In "Send in the Clones," a swarm of helicopters delivers doughnuts to the Homer clones to "Ride of the Valkyries" from Apocalypse Now.
When Homer is riding on Ned Flanders' cow body, he is singing his rendition of "The Lion Sleeps Tonight".
This is the title local news stations give to severe-storm coverage; to warn about the clones this becomes, "Swarm Watch" a parody of "Storm Watch".
In the Send in the Clones segment, when Marge comes back from shopping with a clone of Homer, as this occurs, the top part of one of the arch windows is missing.
When Homer is pulled into the back room by Prof. Frink, the piano music continues even though Homer isn't at the piano playing anymore.When Patty and Selma are shown shooting a grave, the colors of their dresses are incorrect; Patty usually wears red and Selma usually wears blue.
Kaiser Wilhelm's name is mispronounced. As he is German, it should be pronounced like "Vilhelm."