The room the kids meet in is called the Single Purpose Room, a take on Multi-Purpose Rooms that are common in learning institutions.
The scenes with Nelson Muntz removing a latex mask to reveal his true self, which leads to a dissolve with a jigsaw-puzzle fade, are parodies of the 1960s television series Mission: Impossible.
The scenes in the court were a parody of the movie Inherit the Wind.
It is not mentioned that creationism in public schools had already been declared a federal crime in 1987, because it denies the separation of church and state.
This is one of the very few times Ned Flanders had a villianous role. He banned the theory of Evolution and Lisa was arrested for teaching it. However he did apologize to Lisa at the end of the episode and even offered to take the kids out for ice cream.
This is the second time in the series that only Lisa was arrested. However she's not shown in jail implying she was droped off at the Simpsons house.
After this episode ned started respecting other Religons.
Goofs
When Seymour Skinner holds up the textbook "Life In These 38 States", 39 states appear on the cover: the first 38, plus Oklahoma (the 46th state).
Seen from afar in the court room, Lenny has no stubble.
