In addition, "Cosmic Wars: The Gathering Shadow" was an thinly-veiled parody of The Phantom Menace, and the various complaints against The Gathering Shadow strongly resembled various complaints against The Phantom Menace, to a certain extent the entirety of the Prequel Trilogy and the Sequel Trilogy
The character Jim Jam in "Cosmic Wars" is in turn a parody of Jar Jar Binks from "Star Wars Episode I: The Phantom Menace" On a related note, Lisa's statement about Jim Jam being a negative stereotype (as well as Luigi's comments shortly thereafter) refers to criticisms of Jar-Jar Binks being a stereotype of Jamaicans and African-Americans as well as part of the reason he was controversially received.
The Gathering Shadow is a parody of the Phantom Menace and Attack of the Clones.
Homer sings Glen Campbell's "Wichita Lineman" when he puts the AA operator "on hold."
The title of this episode is a play on the film, Independence Day, and Martina McBride’s song, “Independence Day”.
Marge repeatedly hiccupping, rendering her unable to finish the word "incarcerated," and subsequent decision to rephrase her sentence to use shorter words ("I'm going to jail") is a nod to a recurring Porky Pig gag.
The other film airing at the Aztec theater, The Momentum of Things, was a parody of the British-American romantic comedy Brassed Out. Otto's holding Margaret Thatcher responsible for the decline of coal mining was itself a reference to the left-leaning perspective of Brassed Out. Coincidentally, both Brassed Out and the Prequel Trilogy of Star Wars (which was parodied by The Momentum of Things and Cosmic Wars: The Gathering Shadow) featured Ewan MacGregor in a major role.
When Cletus requests to see Cosmic Wars and explains he wanted to see if any aliens in the film matched up with the alien they had in their Root Cellar, he flashed a photograph showing a bound and gagged UPS deliveryman.
The scene where Homer plays the piano, while Marge sings, was cut from this episode and later appears in the episode "Mommie Beerest" during the closing credits.
When Moe cries at the fact he just obliviously sold a expensive bottle of Chateau Latour wine to Homer and Marge, he dries his tears with a lost Shakespeare play, which would be worth much more than the wine.
This is the second episode where a Simpson attends rehab. The first was "Duffless".
A poster for the movie Teenage Sex Wager, which was mentioned in the previous episode, "The Ziff Who Came to Dinner", appears in the background of the opening scene.
When Bart and Lisa are taking the tour, they are sitting at the front of the bus. Seconds later they are at the back of the bus escaping.
When Bart is making a hole, Lisa does not have a pad and pencil then after Marge and Homer takes Lisa is holding them.
When complaining about The Gathering Shadow, Comic Book Guy states that despite viewing it as the worst Cosmic Wars ever, he's nonetheless going to see it three more times that day. However, such would actually be impossible since it is heavily implied that the film lasted the entire day, or at the very least half the day.