King-Size Homer Lisa imagining herself as a morbidly obese redneck is similar to Bart imagining himself as a lardo on workman's comp. Also: Lisa has the same flowery muumuu that Homer wore when he finally gained 300 pounds and went on disability. In the fantasies they both speak in southern accents.
The Simpsons 138th Episode Spectacular: A K.C. and the Sunshine Band song plays during a scene where a male character is naked ("Shake Your Booty" is used during the end montage featuring "hardcore nudity"/"That's The Way I Like It" plays when Apu and Sanjay turn the Kwik-E-Mart into the Nude-E-Mart)
Lisa on Ice: Reference to towel snappings (Homer chases Uter around the locker room and snaps a towel at him/Kent Brockman's report on towel snappings getting worse).
Bart vs. Thanksgiving: A Simpson kid runs away from home and ends up on the news (Bart at the homeless shelter during Kent's report/Lisa on "Smartline")
The Tracy Ullman Show shorts: Homer's line, "Let's go out for some frosty swirls" is similar to Homer's old catchphrase "Let's go out for some frosty chocolate milkshakes."
Mother Simpson: Lisa thinks she's adopted because she's the only smart member of the family.
When Lisa is figuring out the puzzle, one of the clues she rules out is that it's not one of Prince's names, a reference to the period between 1993 and 2000 that Prince changed his name to a symbol and was known as "The Artist Formerly Known As Prince" (or simply "The Artist").
Lisa's story is similar to the book, Flowers For Algernon, about the journal of a mentally disabled man who undergoes experimental surgery to become super intelligent, only to realize the effects were temporary and struggles to preserve his intellect before he relapses into retardation (the Season 12 episode "HOMЯ" would follow a similar plot that Flowers For Algernon does).
A portrait of a 50s Elvis Presley can be seen behind Lisa when she is imagining her future.
Jasper's subplot calls to mind the Frozen Dead Guy Days festival, held annually in Nederland, Colorado. The events of this festival are in homage to Grandpa Bredo, a cryogenically-frozen corpse who, since 1989, has remained in stasis inside a Tuff Shed and inspired two documentaries. It is unknown whether this festival inspired the scenario.
Jasper's note expressing his desire be thawed out "when robot wives are cheap and effective" may be a reference to the 1987 cult film Cherry 2000, in a dystopian future where a man has a gynoid (robotic woman) as a sex object. After accidentally short-circuiting her, he comes to fall in love with a female bounty hunter, learning a real woman is better worth loving.
In the show "When Buildings Collapse," the last building to fall is the House of Usher, a reference to an Edgar Allan Poe book of the same name. The reference was even highlighted when Homer says with barely held back giddiness "Do you think it was gonna fall?" right before its destruction. The building which exploded resembles the infamous Aerial bombing of the abbey on Monte Cassino, Italy, by the United States during World War II.
The show itself when being announced, had the announcer mentioning that it aired on Non-Stop FOX, which was an actual time slot for the FOX Channel during early 1996 through 1997 that during that time did in fact air disaster reality shows (namely When Animals Attack and World's Wildest Police Chases).
The song playing in the background of When Buildings Collapse is the 1812 Overture by Pyotr Ilyich Tchaikovsky.
When Bart hoots this is likely a reference to the crowd hooting at the Arsenio Hall Show that ran from 1989 to 1994
When Lisa writes in her diary about her decreasing intelligence, the end of her arm is for a few seconds drawn over her necklace so that a bead looks incomplete.
When Kent Brockman gives his after thought on Lisa's speech his hair and clothes all have entirely different colors. Since channel 6 is notoriously bad, they could be done at different times.
The Simpson Gene doesn't explain how Herb Powell (who is partially a Simpson) is rich and successful if all Simpson males are doomed to be stupid and useless to modern society. Herb was unaware of his genes and as such could be under a placebo effect. Also it could be argued that he fits into the mold because he did give Homer free reign to design a car which bankrupted Herb.
Also: Homer, Bart, and Grampa have all shown flashes of being book and street smart in past episodes, and it's pretty much established that Homer is dumb because he drinks a lot (and later, because of the crayon stuck in his head) and Bart became a bad student because of how bad his time in kindergarten was as seen on "Lisa's Sax."
The fact about the gene making Homer and Bart stupid is sort of changing the stupid definition because stupidity is not genetic, people often describe stupidity as being unintelligent from making poor decisions and have the ability to be smart. Being unintelligent from family genetics is more of a learning disability.
When Jasper Beardly starts twitching in the freezer, Apu turns the setting from "cold" to "freezing". But since it is a freezer which holds ice cream, its temperature should already be below freezing.
Homer and Bart's candy bars initially have many different colors of wrappers, but after Lisa imagines her potential future, all of the candy bars have red wrappers.
In this episode, Homer eats soup skin, despite that "Bart Gets an F" established that he hated "...that icky soup skin." He could have learned to like it between that time. Also, it might depend on what kind of soup he eats.
The "offensive baseball cap" is colored green when the Flanders children try to read it. However, it is colored blue when the Rich Texan enters the shop.
Luann van Houten is shown with Kirk, even though this episode (in both production and broadcast order) comes after Luann's divorce and her makeover.
When The Rich Texan comes to the Kwik-E-Mart, his appearance is completely different from usual. He has black hair, grey coat and a brownish-green pants rather than his usual grey hair and cream colored coat and pants.
When Lisa goes downstairs to be in the same room with Homer and Bart, the family room is in the location where the living room should be.