The episode includes cultural references to the 1968 song "In-A-Gadda-Da-Vida" by Iron Butterfly, which is played during the show (as "In the Garden of Eden"), and Chilean poet Pablo Neruda, as well as a parody of Judy Blume's 1970 book Are You There God?

Writers from the fields of religion, philosophy, popular culture, and psychology cited the episode in books discussing The Simpsons and the show's approach to the nature of the soul.

Bart experiences several unusual phenomena, such as automatic doors refusing to open for him and no longer finding any humor in Itchy and Scratchy.

After having a nightmare and being taunted by Lisa, Bart again desperately tries to persuade Milhouse to return his soul, going so far as to travel across town after the Van Houten family moved out of their house due to fumigation.

Daniels had originally intended for the song to be "Jesus He Knows Me" by British rock band Genesis, but the producers were unable to obtain the rights for it to be featured in the episode.

Kurt M. Koenigsberger comments in his 2003 book Leaving Springfield that "a good deal of enjoyment" is to be had from the episode, due to "the exposure of the hypocrisy behind 'the finance of salvation' and the ambivalent operations of the commercial world".

[8] Don Cupitt, a fellow of Emmanuel College, Cambridge, believes that when Lisa lectures Bart about the soul, she "shows a degree of theological sophistication which is simply not tolerated in Britain.

"[9] Paul Bloom and David Pizarro wrote in the 2006 book The Psychology of The Simpsons that although Lisa does show "healthy religious skepticism", she still believes in an eternal soul.

[10] However, Lisa tells Bart at the end of the episode, "some philosophers believe that no one is born with a soul; you have to earn one through suffering, and thought, and prayer".

[10] Bloom and Pizarro acknowledge: "Indeed, some philosophers and theologians say that without belief in a soul, one cannot make sense of the social concepts on which we rely, such as personal responsibility and freedom of the will.

[11] Booker cites a scene from the episode where Milhouse asks Bart what religions have to gain by lying about concepts such as the existence of a soul – and then the scene cuts to Reverend Lovejoy counting his money; Booker believes that this implies that religions create mythologies so that they can gain money from followers.

It's just something they made up to scare kids, like the Boogie Man or Michael Jackson", and then suggest questions to ask students, including whether they know individuals that agree with Bart, and their views on the existence of a soul.

[13] In the 2004 book Planet Simpson, Chris Turner quotes Bart's revelation to Lisa that he sold his soul to Milhouse for five dollars and used the money to buy sponges shaped like dinosaurs.

"[14] Turner comments: "Here Bart is the epitome of the world-weary hipster, using the degraded language of modern marketing to sell off the most sacred parts of himself because he knows that some cheap sponge is more real, hence more valuable, than even the loftiest of abstract principles.

"[14] On the DVD audio commentary for the episode, writer Greg Daniels cited Martin Scorsese's 1985 film After Hours as an influence on Bart's night-time trek to retrieve his soul from Milhouse, only to experience a series of unusual encounters.

"[8] Kurt M. Koenigsberger comments in Leaving Springfield: "While Bart may be familiar with the canon of Chilean poetry, the joke takes its force in part from the probability that The Simpsons' viewers are not.

In July 2007, an article in the San Mateo County Times notes that "Bart Sells His Soul" is seen as one of "the most popular episodes in Simpsons history".

[25] In their section on the episode in the book I Can't Believe It's a Bigger and Better Updated Unofficial Simpsons Guide, Warren Martyn and Adrian Wood comment: "Undoubtedly the most disturbing episode of the series, with Bart's nightmare of losing his soul – illustrated by a macabre playground where all the souls of his playmates are visible, and his is tagging along with Milhouse – more frightening than funny.

[29] Lisa's voice actress Yeardley Smith stated in an interview that "Bart Sells His Soul" is one of her favorite episodes along with "Girly Edition".

Club, Erik Adams writes that "If 'Bart Sells His Soul' has anything to say about the value of the human spirit, it's glimpsed in those final moments of Bart and his see-through Buddy ramming into Martin's rowboat.