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.
The trial itself is based on the 1925 Scopes Monkey Trial, which protested the teaching of creationism in public schools, and saw laws supporting it repealed, as appears in the episode.
The song in the creation exhibit at the museum is "what a fool believes".
This is one of the very few times Ned had a villainous role. He banned the theory of evolution and Lisa was arrested for teaching it. However, Ned apologizes to Lisa for his actions and even offered to take her and the other kids out for ice cream.
This is the second time in the series that only Lisa was arrested.
From this episode onwards, Ned develops a greater respect for religions outside of Christianity.
Bart bats left handed.
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.