The solar-powered diesel carries the ATSF (Atchitson, Topeka & Santa Fe Railroad) logo on its front.
Homer's problem with the rat poison, the dog and Maggie is a reference to Fox, goose and bag of beans puzzle form of the River crossing puzzle in Professor Layton & the Curious Village.
This is the Grain, Chicken, Fox puzzle which Cletus asked Homer to help him with until they were eaten and he was left with the fox.
When Homer looked at the camera saying "Can someone help me with this puzzle" it could be a reference to Special Agent Oso.
The main plot of this episode spoofs National Treasure and The Da Vinci Code.
After Benjamin Franklin cuts up the snake, it resembles his Join, or Die political cartoon.
Mr. Burns claims it's his eye (and his pyramid) on the dollar bill.
In another reference to the Da Vinci Code, Mr. Burns calls Smithers his loyal albino servant.
The scene where Kent Brockman loses it on the air during his news segment is a parody of Bill O'Reilly losing it on Inside Edition.
Mr. Burns's quips "Tardy Boys" and "Nancy Clueless" are references to popular children's mystery book series The Hardy Boys and Nancy Drew.
The scene with Sister Marilyn parodies Marilyn Monroe's famous dress-blowing scene over a subway grate in The Seven-Year Itch.
When the sisters landed in America, they were in Philadelphia, Pennsylvania and were greeted by the Phillie Phanatic.
Homer buys rat poison at "Pest Bye", similar to Best Buy.
When Bart turns Springfield into Hell, the swirling whirlpool above the church is similar to how Hyrule Castle appears after Ganon takes over in The Legend of Zelda: Ocarina of Time.
When Lisa, Principal Skinner, and the comic book guy are hanging on the Mr. Burn's helicopter, it is a reference to the Simpsons arcade game when the family hangs on Smithers' helicopter.
The song the nuns are singing as Lisa enters the church is an arrangement of "O Fortuna" by Carl Orff.
The song played after Maggie is set on the throne is similar to "Theme from 'The Mission'" by Ennio Morricone.
At the scene where Lisa finds Principal Skinner and Comic Book Guy at the bell tower, Skinner quotes the reason why they call themselves The brethren of the Quest is because they use Agnes Skinner's Nissan Quest Minivan, which is a real minivan sold in the US.
The scene with Snake stating that the gem has returned to its rightful place might refer to Snake having been an archeologist, and thus have known of this historic treasure.
The scene with the rats in Homer's kitchen is a reference to "Ratatouille". Homer responds by saying "Rats in the kitchen? Just like that delightful movie I taped in the theater". He holds up a DVD with "Ratatouille" spelt as "RATATOOEY".
The rearrangement of "Regally, the rock gem is Lisa" is "It's really Maggie, Sherlock". It references Sherlock Holmes, the fictional detective.
The writing at the Springfield sign do not appear until Lisa mentions it, and it disappears after she solves the anagram.
When Lisa was looking at the Springfield Bell Tower from the park, the top level had only the bell, with two openings on each side. However, when Lisa, Comic Book Guy and Principal Skinner go to the top level, there's another room there and no openings at one of the sides.