The scene of the children pulling the school bus up the hill is a reference to the movie "Fitzcarraldo". When Uter makes reference to the movie, Nelson punches him in the stomach saying "That movie was flawed".
The episode's couch gag (which shows the house, Springfield, the continent, the planet, the Milky Way, and the universe, and finally goes back to Homer's body) spoofs the 1977 science education movie Powers of Ten. The gag was first used in "The Ziff Who Came to Dinner."
When Bart drops his shorts to take a leak outdoors ("The world is my toilet now!"), the music playing is the theme from Born Free.
During the montage showing Bart living with a pack of wild dogs, the music playing is from Vivaldi's The Four Seasons.
At the very end, while the wicker statue burns, the Simpsons play (and dance to) "Tijuana Taxi" by Herb Alpert and the Tijuana Brass.
The wicker statue of Lisa that Bart builds is a reference to the 1973 film The Wicker Man. The notorious 2006 remake came out about ten months after the episode first aired.
Jimbo calls the Lisa statue "The Wicker Witch of the West," referencing both The Wicker Man and The Wizard of Oz.
Bart's plea to Lisa to "Look in your heart" is a reference to the 1990 Coen Brothers film Miller's Crossing.
Samantha Stankey from "Bart's Friend Falls in Love" is clearly visible in the field trip, even though she was sent to an all-girls convent school at the end of that episode. She could have been taken back to the school.
The entire glacier which Lisa causes to sink seems to be floating on top of the lake, even though only 10% of any given iceberg is visible above the surface in reality.
Following around someone on whom you have a restraining order (as Lisa does to Bart) is considered abuse of the order and is grounds for having it removed.
Also, Bart was able to obey the order at the Simpson home, but not at school, which would mean that the school is smaller than the Simpson home. It is impossible for anyone’s house to be bigger than a school.
Also at the end when Lisa throws the restraining order into the fire, you can see it and it says the plaintiff is Bart, and the defendant is Lisa. That would mean that Bart originally filed the order and Lisa had to stay away from him. It was in fact vice versa.