- The episode has many references to the 1961 romantic comedy film Breakfast at Tiffany's:
- The title is a reference to the song "Moon River," which is from the film. The song is also played during the credits, which was also dedicated to Andy Williams who died of bladder cancer on September 25, 2012.
- In two scenes, Mary is dressed as Holly Golightly:
- In one, she is wearing the same black dress and hat with the white ribbon around the hat.
- While playing guitar, Mary is dressed similarly to Holly while she plays guitar, albeit with a red bandanna as opposed to Holly's white.
- In the film, Holly left her "family" to set up a new life in New York, much like Mary does here, though her dad comes to get her, not her husband like in the film.
- Fievel Mousekewitz, the main protagonist of the 1986 film An American Tail is mentioned by Homer who thought that Fievel was his ancestor.
- The couch gag is a reference to the The Longest Daycare.
- Pappa Pia! is a reference to the musical Mamma Mia!.
- Death of a Salesman: The Seussical is a parody of the 1949 play Death of a Salesman and, The Seussical play.
- Samsun is a parody of Samsung.
- LC is a parody of LG.
- Milhouse references Sesame Street and Oscar the Grouch.
- The September 11 attacks was touched upon slightly when Bart tells Homer that he "would love New York, now that [his] two least favorite buildings have been obliterated." Bart then quickly adds "Old Penn Station and Shea Stadium," after a pause.
- George Tooker’s painting Subway (scene when Bart and Homer enter the subway).
- This is the second time the Simpsons family travelled to New York City. The first time was in "The City of New York vs. Homer Simpson".
- The patterns on Simpsons family wings (they were butterflies in a couch gag) were:
- The items in Bart's box of "precious junk" include:
- The banner on the theatre's Pappa Pia! advertisement reads "The story continues, because ABBA has more songs."
- The names that appear in the listing of Mary Spuckler's apartment include:
- T. Bickle (Travis Bickle was the main character from "Taxi Driver")
- Mary Spuckler
- H. Golightly (Holly Golightly was the main character in "Breakfast at Tiffany's").
- With eleven guest stars, "Moonshine River" and "Homer at the Bat" currently hold the record for highest number of guest stars in one episode.
- Gina is the only one of Bart's ex-girlfriends who punches Bart.
- In New York there is an ad that appears Canyonero car, the car that promoted Krusty the Clown in the episode The Last Temptation of Krust.
- In syndication, the Create-A-Couch-Gag Contest promo is omitted.
- Greta Wolfcastle and Shauna Chalmers are the only ones of Bart's girlfriends so far that we don't see in this episode.
- Lisa is playing a Tuba instead of her saxophone in the opening sequence.
- Bart's previous girlfriends:
- Adverts that are seen from previous objects featured in the show:
- The Khlav Kalash and the Khlav Kalash vendor from "The City of New York vs. Homer Simpson" appear again as a restaurant in New York City.
- Sideshow Bob returns and tries to kill Bart, but his plan is less elaborate.
- In the queue for the Romeo and Juliet play, many of the people standing in line appear in the line more than once.
- Although Homer personally hates New York, he is delighted to go to New York in this episode.
- In the taxi scene, the hobo closes the car's door when he leaves, but when Homer tries to sneak up to leave Bart in the cab, the door is open again.