The title is a reference to the Christian sign of the cross: In the name of the Father, the Son and the Holy Ghost (Spirit).
Marge's ringtone is the theme tune to Hawaii Five-O.
The song that Homer, Bart and the other Catholics are dancing to in Marge's dream is Riverdance by Bill Whalen. This song is also played in the credits.
The lyrics that Otto sings on his lute are a metaphor for oral sex, and not a tough metaphor either, "Dragon in my dungeon, Maiden in my lair, There's potion in my wizard's pot, Now drink it if you dare."
Homer confuses Plutarch with Mickey Mouse's dog, Pluto.
This is the second time in the series that Bart is expelled from school after "Whacking Day".
The ragtime music video playing during the montage of Homer and Bart at the Catholic school is called "Maple Leaf Rag," a public-domain ragtime piano piece composed by Scott Joplin in 1899.
Statue plaque: "St. Jerome. He suffered for our sins. Now it's your turn."
Catholic Springfielders: It is made clear in this episode that most of the main characters in Springfield are Protestants, who attend Rev. Lovejoy's church. The episode does give some insight into who are the (probable) Roman Catholics in Springfield. At the church's pancake dinner one can spot: Bumblebee Man (Hispanic); Mayor Quimby (Irish, but he may only be attending a community event for political reasons); Luigi and two members of Fat Tony's crew (Italian). Fat Tony is sitting at a different table as his fellow mob members.
Homer thinks that Mickey Mouse's dog Pluto is called "Plutarch".
Homer asks how Catholics can stand not eating meat on Fridays, but this practice is no longer mandatory for Catholics, except on Good Friday.
This episode was nominated for the 2006 WGA Award (TV) for Animation.
Bart's Book: Who Made The Barrel? You Did.
This is the third time a Simpson family member attempts to convert to a new Religion and Marge, Ned, and Reverend Lovejoy attempt to bring that family member back. The previous episodes were "The Joy of Sect" and "She Of Little Faith".
It is made clear that the Simpsons and most of the characters in Springfield are Protestant.
Originally scheduled to air April 10, 2005. It was pulled due to the death of Pope John Paul II the previous week.
She of Little Faith is referenced when Marge wants to convert Bart back to her religion.
In "Lisa Gets an "A"", Bart asked Marge if they can go 'Catholic'. In this episode he becomes a Catholic. Bart also begs Homer to reconsider sending him to military school by telling him he will find religion, while in this episode, Homer plans to send Bart to the army if he gets expelled from Catholic school.
Bart says he could convert to Judaism, while singing "Don't have a cow man, don't have a cow man, have a fish instead" to the tune of hava nagila.
It is never explained how Bart goes back to Springfield Elementary. Although one theory is that Rev. Lovejoy must have bribed or forced Skinner to take Bart back
Lisa states that Latin is Plutarch's language. However, Plutarch was a Greek who wrote in Greek during the Roman Empire.