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The zombie invasion of Springfield could be any zombie work, but it's most likely a reference to Night of the Living Dead.
The background fight between a giant robot and a giant monster is a reference to Pacific Rim.
Lard Lad being zapped by lightning and coming to life is a reference to Treehouse of Horror VI.
The giant Wiggum-Cyclops is based on the Cyclops from The 7th Voyage of Sinbad.
Alfred Hitchcock's cameo, and the crows perched all over a climbing frame before attacking Krabappel, reference Hitchcock's film of The Birds.
Bart and Stephen King writing " All work and no play makes Jack a dull boy" is a reference to Stanley Kubrick's version of The Shining. The first segment of Treehouse of Horror V is a homage to The Shining.
Groundskeeper Willie's appearance is a reference to Hellboy, while his fight with Kroenen is a reference to the film.
Homer's mutated appearance is a reference to Blade II, the monstrous Reapers and Explosm.net:Cyanide & Happiness #1126 while Carl's costume references Blade himself.
Corpses of the 'Tracey Ullman Show' versions of the Simpsons family can be seen underneath the Nuclear Power Plant, as well as Godzilla's skeleton. This is actually the second episode where corpses of the Tracy Ullman Show versions have been shown underground, following Adventures In Baby Getting.
Mr Burns and Smithers resemble, respectively, the Pale Man and a fairy from Pan's Labyrinth.
Items on the store checkout resemble devices from the film Cronos and Hellboy 2: The Golden Army.
Maggie is priced at the checkout as 666, the 'number of the beast'.
The resemblance of the store cashier, Marge and Baby Gerald as oversized cockroaches is a reference to the film Mimic.
The school band features: the original 1916 Phantom of the Opera, the 1925 version, 1943 version, and 1962 version. Mr. Largo, however, resembles the Phantom of the Paradise.
As Lisa leaves the music room, paintings are hanging on the wall showing: the alien Maggie from Treehouse of Horror IX's Starship Poopers, Dr Hibbert and human-animal hybrids from Treehouse of Horror XIII's The Island of Dr. Hibbert, Homer as the Raven-tormented narrator Treehouse of Horror's The Raven and the Grand Pumpkin from Treehouse of Horror XIX's Milhouse and the Great Pumpkin.
Cthulhu makes an appearance; this may also be a reference to Guillermo del Toro's planned film of At the Mountains of Madness.
Horror/science-fiction writers HP Lovecraft, Edgar Allan Poe, Ray Bradbury and Richard Matheson all make a cameo, doing things relating to their works: Lovecraft (author of the Cthulhu Mythos) drinks tea with one of Cthulhu's tentacles, Poe (author of The Raven) feeds a 3-eyed raven, Bradbury (author of The Illustrated Man) draws on a tattooed man, and Matheson (author of I am Legend) stands next to one of the novel's vampires.
The mob of classic monsters chasing Bart and the others consists of: Boris Karloff's Frankenstein's Monster, Bela Lugosi's Dracula, Lon Chaney Jr's the Wolfman, the Metaluna Mutant from This Island Earth, Karloff's Mummy, Gillman from Creature from the Black Lagoon, the Bride of Frankenstein, and Claude Rains' Invisible Man.
Maggie drives the sedan from the movie The Car attempting to run over Milhouse. Homer also considered running over Milhouse in the "I Know What You Diddily-Iddly-Did" segment of Treehouse of Horror X.
Characters appearing in the panning shot are: the plant god from Hellboy II, Rod Serling (Twilight Zone creator/narrator), the robot from Lost in Space, the Man in the Beaver Hat from London After Midnight, the titular creature from Alien, the Ymir from 20 Million Miles to Earth, one of the Mole People, the skeleton soldiers from 1963's Jason and the Argonauts, the creature from The Thing from Another World, a Morlock from The Time Machine, Ro-Man from Robot Monster, Cavor's craft from First Men in the Moon, Count Orlok from Nosferatu, aliens from Invasion of the Saucer Men, the Fly, Klaatu's spaceship and the robot Gort from The Day the Earth Stood Still, two of the 'freaks' from Freaks, and Rondo Hatton from House of Horrors.
In the panning shot, Hans Moleman is seen painting the Alfred Hitchcock Presents / Shamley Productions logo on a wall.
The wall that Moleman is painting on has "El Muerto" painting on it, possibly a reference to Bart's "el Barto" signature and Dia de los Muertos.
In the couch gag, Homer resembles the ghost Santi from The Devil's Backbone.
Lisa falls down an Alice in Wonderland-style portal, wearing Alice's iconic costume.
Hypnotoad from Futurama makes a cameo appearance.
The final segment references Pan's Labyrinth again: the throne room is the same, Marge and Homer resemble the King and Queen of the underworld, Lisa is dressed as protagonist Ofelia, there are small fairies flying about, and Bart resembles the Faun.
Oh, the Places You'll D'oh is a parody of the Dr. Seuss book, , to, among other things, The Cat in the Hat The Lorax (which is a parody of the Borax), How the Grinch Stole Christmas!, Yertle the Turtle and other stories, The Sneetches The 500 Hats of Bartholomew Cubbins What Was I Scared Of? Green Eggs and Ham, Horton Hatches The Egg and the title of another Dr. Seuss book of all is, , the final book he made.
Oh, the Places You'll Go The mask The Fat in the Hat wears when blowing up city hall looks similar to Guy Fawkes Mask from the movie V for Vendetta.
At the end of the segment, The Fat in the Hat says not to let him be played by Mike Myers, a reference to the fact that Mike had played the title character in the
live-action adaptation of The Cat in the Hat. Dumbo An elephant named Jumbo gives Moe a shower.
Dead and Shoulders is a parody of the film, , and the title is a parody of the shampoo brand, The Thing with Two Heads .
Head & Shoulders Freaks, No Geeks is a parody of the film, , and the title is a parody of the short lived show, Freaks .
Freaks and Geeks The scene of Rabbit ears and bigmouth is a parody of Futurama
The last scene where Homer says "And that, kids, is how I met your mother" references the show, , and its theme music plays over the credits.
How I Met Your Mother When Krusty is the funny man he says "Seriously folks, I really think we shoud stop this " and everyone laughs.
Freaks, No Geeks was supposed to take place in 1932 but when Homer tells the kids his story it's in the present time. Since this is non canon, he could have lived for 81 years after the incident but it says in the last article that he died. He must've faked his death at the time.