The song played on the tape recorder is "A Horse With No Name" by America. When Lisa hears the song, she refers to it as "county fair music".
The scene where Martin illustrates in front of the other children that individually they are weak (by breaking a single twig), but as a bundle they are unbreakable (like a bundle of twigs) is from the legend of the dying Bulgar ruler khan Kubrat talking to his sons.
Actors dressed as Spider-Man and Dr. Octopus make an appearance at Nelson's party.
Lisa's fantasy book is mostly a reference to Harry Potter, specifically the sixth book, Harry Potter and the Half-Blood Prince, with Greystash being a parody of Dumbledore. It also contains elements of The Chronicles of Narnia and Deltora Quest while Angelica's trap, a giant hourglass, is similar to Disney's Aladdin. Malicious Crump, the wizard that kills Greystash is a parody of Lucius Malfoy (Lucius(-cious-) Malfoy(-Mali-)).
The scene which follows Bart and Nelson as they enter the cafeteria through the back of the school and through the kitchens while Bart acts as a narrator is a direct parody of the celebrated three-minute tracking shot from Goodfellas which shows Henry and Karen Hill as they enter a nightclub through the back accompanied by Henry's narration. The song played is "He's a Rebel" by The Crystals; another Crystals song, "Then He Kissed Me", was used in the actual scene from Goodfellas.
When Bart comes to Nelson's home after he had played with Milhouse, Nelson gets outraged, breaks his camera and says "Look what you made me do!" This is parody of Stephen King's movie Misery.
The scene with Nelson's vest and picture in the closet is a reference to the end of Brokeback Mountain with the guitar music of Gustavo Santaolalla.
The scene in which Bart and Milhouse play with kites may be a reference to The Kite Runner.
Bart was wearing rubber boots when he was on that trip to the tide pools.
Marge makes Bart attend Nelson's party, while in "Bart the Mother", she forbade Bart to go near him. This matter could have to do with Marge and Nelson getting along with each other in "Sleeping with the Enemy".