This episode is notable for featuring the Seven Deadly Sins:
Lust: Homer and Marge remember making out to In-A-Gadda-Da-Vida (In the Garden of Eden) and everyone in church looking sweaty and disheveled as if they just had sex.
Gluttony: When Moe is converting his bar into a restaurant, he acquires a gigantic deep-fat fryer, claiming it can deep-fry a buffalo in forty seconds, to which Homer grouses, "Oh, I want it now!" Later, Homer gets Bart's meal at Moe's Tavern.
Greed: Reverend Lovejoy counting church collection money, Milhouse avariciously celebrates owning Bart's soul, saying, "Who's stupid now?" Moe starting a restaurant because restaurants make more money than bars, Homer's brain telling him, "Quiet, you fool! It can be ours!" when Bart leaves his dinner sitting out (see also Gluttony).
Sloth: Bart and Milhouse slacking off cleaning the organ.
Wrath: Reverend Lovejoy gets angry at being fooled; Moe screams at a little girl who says her "sodie" is too cold; Bart gets angry at Lisa when she starts praying for everyone's soul.
Envy: Moe envies the profits of family restaurants. Lisa wants five dollars after Bart tells her he had five dollars. Bart envies the kids in his dream for their souls.
Pride: Bart being too proud to believe he has a soul -- until all of the strange things happen that make him believe that he really did lose it.
Bart saying that a soul is something adults make up to scare kids "like the Boogeyman or Michael Jackson" is a reference to a case in 1993 where Michael Jackson was accused of child sexual abuse (though Bart should already know that Michael Jackson does exist, as seen in "Stark Raving Dad" and the "Dial Z for Zombie" segment of "Treehouse of Horror III," which had Bart use a Thriller album sleeve as a hat during his zombie resurrection spell).
Moe reads a book titled Your Gimmicky Restaurant by Benngian and Fuddrucker. The authors' names are references to the restaurant chains Bennigan's and Fuddruckers.