The Imperial March from The Empire Strikes Back plays while Mr. Burns surveys his monitors in his office. Throughout the series, this is used as a semi-official piece of music for Mr. Burns.
As a subplot in the story, Bart cries 'wolf' to get out of a test, in reference to The Boy Who Cried Wolf. Also befitting the subplot is that Bart is not believed when he is attacked by an actual wolf.
Lisa claims that Pierre and Marie Curie both died of radiation poisoning. Lisa is half right: Marie Curie died of radiation poisoning. Pierre, however, died of a skull fracture after getting hit by a horse-drawn carriage.
When Homer points at the donut delivery guy, his right shirt cuff is colored yellow for a moment.
Groundskeeper Willie tore his shirt off when he was about to go one on one with the wolf, but when Willie tells Bart to go back to class, you can see that Willie has a (ripped) shirt on.
During the scene where Homer and the other Power Plant workers are confronting the Donut Delivery Guy, Homer's hat turns from red to blue.
When Tom Jones performs for Marge and Homer, he has a chain on his ankle preventing him from going very far. However, he kisses Marge even though he shouldn't be able to go that far because of the chain.
When the show first aired, Mrs. Krabappel tells Bart that he faked every illness he could think of to get out of taking the test, including Tourette's Syndrome (with Bart snarling, barking, and making inappropriate comments at Mrs. Krabappel). This caused a lot of controversy with viewers, including one who had Tourette's and threatened to sue the show for its unflattering depiction of the condition. When the show reran during the summer, the "Tourette's Syndrome" reference became "rabies" and Bart's snarling and barking was cut. In syndication, the "Tourette's Syndrome" reference was reinstated, but not Bart's snarling and barking. On the season four DVD set and the reruns shown on FXX, the "rabies" line is used, yet Bart's snarling and barking was reinstated. About the only place the original version exists is on English-speaking international versions shown in the United Kingdom, Australia, and New Zealand.