Lisa creates a small pig from a rubber eraser and push-pins, which was featured in a Life in Hell comic strip.
Despite airing in season nine, this episode has the production code 4F24. The 4F production line is for episodes that have aired (or were meant to air) during the eighth season.
In large part because of this, there was a reference to Non-Stop FOX, which was still a timeslot when the episode entered production, but had been removed by the time the episode aired.
When the children try to solve a brain teaser, only Martin, Milhouse and Nelson do it. Bart only shows Milhouse's solution written on the piece of paper to Martin.
The can in Freak-e-Mart can be a reference to Artist's Shit.
The baseball cap probably says Show me your taps.
It's possible that Homer doesn't suffer from the Simpson gene but only does from the crayon in his brain as seen in HOMЯ.
Previous Episode References
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).
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 Arial 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).
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: 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."
And Lisa should have known that the women on Homer's side of the family are smarter than the men, since she met Homer's mom on Mother Simpson and, aside from yelling "D'oh!" whenever she gets hurt, Mona was actually very smart. That doesn't count because Homer's mother isn't a Simpson by birth.
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.
The couch gag: The only fruit that can actually grow on a vine in real life would be the yellow squash (Homer) [A squash is technically a fruit, though for culinary and trade reasons, it's classified as a vegetable]. Strawberries (Bart), asparagus (Marge), broccoli (Maggie), and pineapple (Lisa) are not vine produce.
Kent Brockman doesn't recognize Lisa, even though she was on "Smartline" before, as seen on "Lisa the Skeptic."
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.
Homer gathers his relatives from the tri-city area, but Shelbyville is the closest city to Springfield (unless Homer also meant Capital City, and combined with Springfield, would make it three).
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.
On the TV, it states that the channel/network is "Fox" but soon after, it states that it is on Channel 6 (the local news).