Lisa thinks of Nancy Drew and the Hardy Boys while trying to figure out a way to get back the school key. Due to the time since the books were originally created, they have all perished except for Nancy, who is dead by the time Lisa gets the key duplicated.
The scene where Nelson repeats, "And the day before that", while also walking backwards is a reference to the SpongeBob SquarePants episode, The Algae's Always Greener, where Krabs says "And the next day" repeatedly to Plankton. Also, Nelson speaks through the loudspeaker, which is similar to when Krabs speaks to Plankton on the phone.
The quote by Chief Wiggum when the police blimp crashes, "Oh the Zoo-manity!" is a reference to the Hindenberg disaster. Zoo-manit by Cirque Du Soleil was mentioned by Bart in "Marge's Son Poisoning".
In the fake classroom there is symbols for the four elements (Fire, Air, Earth, Water) visible, as depicted in Avatar.
This is the second episode where Chief Wiggum fails to catch something going between his legs. The first was "Coming to Homerica".
This is the second episode to show Otto crashing a bus full of children off a bridge and into a water source. Otto previously did so in "Das Bus", but on that occasion, the kids on the bus got stranded on a deserted island.
When Lisa enters the banned book room for the first time, a hamster corpse in an orange transparent ball can be seen. This is a possible reference to the Deweys' hamster in Malcolm in the Middle. It might also be Superdude, from the episode "Skinner's Sense of Snow" and died in "Who Shot Mr. Burns? (Part One)".
This is the second time Lisa has found a hidden room inside Springfield Elementary, and when she shows others the room, a false wall was built to hide the hidden room (the first was "Grift of the Magi").