The problem Homer faces in crossing the river is a classic logic puzzle, originally involving a fox, a duck and a bag of corn in place of the dog, baby and poison. Cletus' cameo refers to the original puzzle.
The Springfield Bell Tower was probably drawn as a nod to the bell tower of Mission San Juan Bautista from Alfred Hitchcock's masterpiece Vertigo (1958)
The title "Gone Maggie Gone" is a play on words of the similar "Gone Baby Gone", a novel written by Dennis Lehane about the faked kidnapping of a woman to get back at her husband. This novel was also turned into a movie of the same name. Since Maggie is also a baby, this gives the title an extra link to the novel.
The opening sequence identifies this episode as a 'Da Vinci Code' spoof, but the references to America and the Freemasons may relate to 'The Lost Symbol,' another Dan Brown novel featuring codes and puzzles.
When Homer has to cross the river in a boat with Maggie, Santa's Little Helper and the jar of poison he discovers they are too heavy to cross together and he needs to figure out which combination would allow for all three to cross safely. This is a reference to the famous "Fox, goose and bag of beans" puzzle that requires similar logic to his solution.