|Treehouse of Horror XIII||
- This is the final Halloween episode where the title says "The Simpsons Halloween Special." Starting with Treehouse of Horror XIV, the words "Treehouse of Horror" will be in its place in the title before the roman numerals.
- The Opening from Lisa's Substitute is used.
- Seen among the crowd of Homer's clones are the following:
- Peter Griffin from Family Guy (who is often compared to unfavorably by detractors of Family Guy as a Homer Simpson clone)
- The original Homer from The Tracey Ullman Show (He says, "Let's all go out for some frosty chocolate milkshakes.")
- A Homer with black glasses (the same ones he found in the toilet in "$pringfield (Or, How I Learned to Stop Worrying and Love Legalized Gambling)".
- A Homer with no face
- A skinny, badly-drawn Homer
- 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 in the island
- Homer - Walrus
- Fat Tony - Beaver
- Kearney - Mandrill
- Jimbo - Parrot
- Marge - Panther
- Bart - Spider
- Lisa - Owl
- Maggie - Anteater
- Blue Haired Lawyer - Moose
- Gil Gunderson - Giraffe
- Mr. Burns - Fox
- Mr. Smithers - Flamingo
- Principal Skinner and Mrs. Skinner - Kangaroo and Joey
- McCallister - Crocodile
- Milhouse - Snail
- Raphael - Chameleon
- Old Jewish Man - Vulture
- Miss Springfield - Racoon
- Lenny - Pelican
- Chip Davis - Gorilla
- Carl - Armadillo
- Krusty - Lion
- Moe - Toad
- Cletus - Sloth
- Chief Wiggum and Sarah Wiggum - Pigs
- Nelson - Wolf
- Otto- Camel
- Professor Frink- Turkey
- Mayor Quimby - Panda
- Manjula - Antelope
- Reverend Lovejoy- Coyote
- Snake - Skunk
- Kent Brockman - Rhino
- Selma - Elephant
- Arnie Pye - Eagle
- Patty - Mountain lion
- Jasper - Goat
- Kirk Van Houten - Aardvark
- Lindsey Naegle - Meerkat
- Dolph - Tiger
- Grampa - Rooster
- Dr. Nick - Squirrel
- Herman Hermann - Lizard
- Sideshow Mel - Lemur
- Judge Snyder - Hippo
- Cookie Kwan - Deer
- Squeaky Voiced Teen - Donkey
- Hans Moleman - Turtle
- Comic Book Guy - Ram
- Martin - Sheep
- Dewey Largo - Bat
- Allison Taylor - Zebra
- Groundskeeper Willie - Orangutan
- Rich Texan - Buffalo
- Helen Lovejoy - Horse
- Mrs. Krabappel - Hyena
- Duffman - Koala
- Disco Stu - Shrew
- Eddie - Dog
- Lou - Cheetah
- Rod and Todd Flanders - Penguins
- Ned Flanders - Cow
- Wolfcastle - Rabbit
- Apu and the octuplets - Possums
- Barney Gumble - Warthog
- Gary Chalmers - Bear
- Luigi - Guinea Pig
- 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.
- In "Treehouse of Horror VIII", Bart gained the body of a fly, in this episode he gained the body of a spider.
- This and the previous Halloween special feature a character transformed into a centaur.
- The Island of Dr. Hibbert is a parody of The Island of Dr. Moreau.
- As an owl, 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 film 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."
- Homer Simpson makes many clones of himself that he must get rid of, and how Pinkie Pie also make many clones of herself that she must get rid of from the My Little Pony: Friendship is Magic episode Too Many Pinkie Pies.
- Peter Griffin from Family Guy is seen standing in a field full of Homer Simpsons 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.
- The Phineas and Ferb episode is a spoof on the famous Simpsons episode of "Send in the Clones".
- When Homer is singing his redintion of The Lion Sleeps Tonight from The Lion King he is riding on Ned Flanders's cow body.
- 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."