It was revealed in the commentary for the episode, that Sara is named after one of Mike Scully's daughters.
It's worth noting that Lisa confronts Marge about her not being transferred to the third grade, yet in the episode "Bart vs. Lisa vs. the Third Grade" she actually was transferred and found herself not ready for this step.
When Bart creates his diversion towards the end of the episode, Milhouse's glasses are still damaged from his jump from the dam.
The scene where a federal agent confronts Milhouse at a dam is identical to a scene from the 1993 movie The Fugitive. The agent resembles Tommy Lee Jones' character and uses he signature line "I don't care."
Marge is seen reading (and fantasizing about) a romance novel titled Love in the Time of Scurvy, which is a reference to Love in the Time of Cholera by Gabriel García Márquez.
When Marge asks him if his earring means he's a pirate, he says, "Kinda". In the latter 20th century, a man wearing an earring was often used to signal homosexuality. By "kinda", he is referring to the pejorative "butt pirate".
Homer's "In America" speech while guarding his sugar pile comes from Scarface.
The speech patterns of the beekeeper voiced by Hank Azaria are based on Adam West's portrayal of Batman.
The company "Goldsboro's Honey" is a reference to easy listening performer Bobby Goldsboro, who had a #1 hit in 1968 with the song "Honey."
Lisa's nightmare features her playing in a band with famous backup artists: Art Garfunkel, John Oates and Jim Messina. The concert is sponsored by Avis, the number two rental car company whose famed slogan is "We Try Harder." The song "Born to Runner-Up" is a parody of "Born to Run" by Bruce Springsteen, who never topped the Billboard Hot 100 charts. Springsteen's highest charting song was 1984's "Dancing in the Dark," which topped out at number two.