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.
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.
This is also a possible "bait-and-switch" reference to "The City of New York vs. Homer Simpson", in which Homer couldn't get his boot off the car because the only restroom he could use was on the observation deck of the World Trade Towers.
George Tooker’s painting Subway (scene when Bart and Homer enter the subway).
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. A synopsis listed on the older FXX app implies that Greta was intended to appear instead of Nikki. It's possible that Reese Witherspoon was unavailable.
Lisa is playing a tuba instead of her saxophone in the opening sequence.