- The premiere of this episode was watched by 18.5 million people in America.
- The title and plot are both references to CHAЯLY, a 1968 film based on the 1959 Daniel Keyes novel Flowers for Algernon.
- The Sick, Twisted, and Totally F***ed Up Animation Festival may be modeled after Spike and Mike's Sick and Twisted Festival of Animation.
- A statue of The Iron Giant can be seen in the festival, this is a tribute to the Oscar-winning director Brad Bird who used to work for the show before.
- The clay animation watched by Flanders and his kids, The New Gravey and Jobriath, is a parody of Davey and Goliath, a similarly Christian-themed animation. This is one of the few scenes in the show to depart from traditional cel or cel-style animation.
- "Gravey" intends to blow up Planned Parenthood, a pro-choice collection of organizations.
- The stand behind Flanders and his kids reading "Animation Today" has imagery of Wallace, Gromit and Feathers McGraw as a reference to Nick Park's second "Wallace and Gromit" short "The Wrong Trousers".
- The voice actor who copies other characters' voices and celebrity voices at the animation festival references how many early Hanna-Barbera "funny animal" characters' voices were often based off popular celebrities of the time. In an ironic sense, Professor Frink points out how one such character obviously has a voice based off Jerry Lewis, just as Frink's voice is.
- The faux old footage of Itchy & Scratchy advertising for Laramie Cigarettes is likely a reference to the first season of The Flintstones, when commercials aired featuring Fred and Barney enjoying Winston Cigarettes.
- Eddie "Rochester" Anderson is seen smoking with Itchy and Scratchy in the above commercial.
- Ozmodiar, a parody of The Great Gazoo from The Flintstones, appears twice during this episode, once after Bart says cartoons do not have to make sense, and once more after all the employees are laid off from the plant.
- Homer blames eBay (rapidly gaining fame at the time this episode premiered) for the poor-quality cowbell he purchased.
- Intelligent Homer solves multiple Rubik's Cubes in his spare time.
- The film Love is Nice, starring Julia Roberts, Richard Gere and Bill Pullman (but not Bill Paxton) is a parody of the other Roberts and Gere films, Runaway Bride and Pretty Woman.
- The line "Is that your final answer?" refers to Who Wants to Be a Millionaire.
- When the researchers examine the x-ray of Homer's brain, they use a visual enhancement machine similar to the one used by Deckard in Ridley Scott's film Blade Runner.
- The name of the animation firm, Animotion, is probably taken from the band known for their 1985 hit "Obsession".
- The animated dog that dances to Homer's movements during the Animotion process resembles Snoopy.
- During the couch gag in the opening credits, Fry from Futurama is dropped onto the sofa, before being sucked away again.
- While mailing his suggestions in the suggestion tube, Homer is humming Johann Sebastian Bach's Concerto Brandenburg #3.
- When the Simpson family visit the animation convention, Bob and Larry from VeggieTales are shown on one of the booths.
- This episode is referenced in The Simpsons comic "Laughter is not the Best Medicine". Dr. Hibbert shows an X-Ray of Homer's head and the crayon is seen.
- Moe, who says he is an unlicensed surgeon, describes his procedure as "the old Crayola oblongata". This refers to the Medulla Oblongata, the lower half of the brainstem.
- In Homer's fantasy of stock ownership a giant gorilla in shackles, wearing a green top hat and holding fistfuls of cash is a reference to King Kong.
- In the anime Bart watches the final scene is a reference to the Japanese flag.
Previous Episode References
- In the previous episode, Bart said he was going to miss the Itchy and Scratchy episode where they finally kiss the Laramie Cigarettes advert, Homer and Marge are watching, starts with the former pair kissing. It's possible he was referencing a real kiss, rather than a staged one, or that the advert doesn't count as canon to the rest of I&S
- The last time Homer got thrown out of the movie theater for spoiling the ending of a movie he found predictable was Colonel Homer.
- This episode contradicts the events of Lisa the Simpson, in the latter, Abe reveals that Homer became stupid at the age of 8, when his Simpsons Gene kicked in. In this episode, it is revealed that Homer became stupid at the age of 6, when a crayon he stuck up his nose got stuck in his brain.
- In Simpson and Delilah, Homer, while watching Jeopardy!, incorrectly guesses that the capitol of North Dakota is named after the German leader Hitler, not Bismarck. In this episode, the newly smart Homer proves his intelligence to his family by correctly guessing Bismarck as the capital of North Dakota.
- Burns Verkaufen der Kraftwerk - Homer buys shares of a share company. In the aforementioned episode he had bought them for 25 cents and selled for 25 dollars (being unaware that They are worth 5 200 dollars) but in this episode he buys 500 of them for unknown price but doesn't get any dividend due to Animotion company going bankrupt.
- Hurricane Neddy - a Simpson is solving Ribuk's Cube. In the aforementioned episode it was Marge solving it and wasn't doing well due to family members talking over each other but in this episode Homer solves several of them and manages it.
- Lisa the Vegetarian - Marge makes a remind that Lisa doesn't eat meat.
- Homer vs. the Eighteenth Amendment - Moe turns his bar into different type of business. In the episode he turns it into a pet shop but in this episode he turns it into hospital.
- Lisa the Beauty Queen - Barney mentioned that he earns money upon being a experimental rabbit.
- El Viaje Misterioso de Nuestro Jomer (The Mysterious Voyage of Homer) - Homer walks past some signs in the dark and is facing sad.
- According this episode, Moe knows some kind of surgery, at least knows how to insert a crayon in Homer's brain.
- A phone number of Moe's plastic surgery is [tel:800-555-0000 800-555-0000].
- This episode can be seen in the 2002 film Trapped.
- A running gag in this episode was someone hitting Homer in the head with a plank of wood.
- A Lego Dr. Hibbert included Homer's x-ray from this episode.
- This is the first episode to air in 2001.
- This is the final episode to have a "BABF##" production code. It took three years (1999, 2000, 2001) to show all episodes with the "BABF##" production code, with most of those episodes airing in 1999 or 2000.
- The crayon was never found because Dr. Hibert always had his thumb over it on the X-rays he showed.
- Though his intelligence increased, Homer didn't gain a better understanding of a long-term plan. Though everyone was laid off at the time, they would have gotten their jobs back once the plant safety was brought up to code.