The entire School Train sequence is a parody of the intro to the '70s music television show Soul Train.
In a hallucination, a train resembling the I Choo-Choo Choose You Train from the episode "I Love Lisa" gets run over by Otto's school train and pressed.
Clearazit is a reference to Clearasil, an American brand of skin care medication.
Marge thinks she is capable of ending bullying, as she "was able to open up another register at Kroger's", Kroger's is an expensive grocery store. Homer is worried because they don't have Kroger's money.
When Krusty asks his writers for jokes to use in jail, one of them replies "How about Orange is the New Blecch". This was actually a punchline used by humorist Jon Stewart on The Daily Show when joking about the fact of Texas Governor Rick Perry going to prison. The phrase is a play of words with Orange Is the New Black, the comedy-drama series.
When Homer talks about vacuuming, Dr. Raufbold mentions billionaire James Dyson. Dyson is best known for inventing a type of bagless vacuum cleaner.
Dr. Raufbold sarcastically compares Homer's mind with the Louvre.
During the bully therapy, Gary Chalmers says his father was a psychologist and a big believer of B. F. Skinner methods. He made his son go through a maze to get his breakfast.
Dr. Raufbold wants Homer to find out why he hated Ned. Homer wants the doctor to tell him the answer and Raufbold replies that nobody told Indiana Jones what he was facing in every movie.
The melody that is heard when Homer kneels in front of the Flander's house strongly resembles the main recurring theme of Philip Glass' Koyaanisqatsi album.
At the end of the episode, in another acid trip sequence, Otto's school train meets The Magic School Bus, Ms. Frizzle and the kids from the show. They enter his ear with the Magic School Bus' magic but Otto pulls them out and squishes them.
The train in Otto's acid trip has a voice similar to Ringo Starr, referencing Thomas the Tank Engine which Ringo narrated in the first two seasons.
When Chief Wiggum is arresting Jimbo, he removes Jimbo's cap to reveal that he still has his hair, conflicting with incidences in "Moms I'd Like to Forget" and "Beware My Cheating Bart" where we see that the top of Jimbo's head is actually bald under his cap.
Flanders' dog Baz, introduced in "Peeping Mom", is seen.
