The couch gag begins with the family entering four chambers that slide into the wall. The technician has to make an extra effort to close Homer's chamber door.
After a bright flash, we see the Simpsons as they would appear as Na'vi.
In a recreation of the scene where Jake Sully tries to capture his own Ikran, the Simpsons run to a cliffside where they see that the skies are filled with flying couches.
Homer jumps from the cliff and fails to catch one of the flying couches. Bart makes an attempt and succeeds.
After the rest of the family climbs aboard the couch, it settles in front of a television and the family puts on 3-D glasses (except for Bart).
Bart sticks Homer's ponytail into a wall outlet, shocking him, and then puts on his own 3-D glasses.
After an executive disembarks from the Fox News helicopter, the copter wobbles and crashes while the pilot cries out, "We're unbalanced! It's not fair!", punning the channel's slogan "Fair and Balanced".
When Smithers leaves Cheney's employ to return to working for Mr. Burns, Cheney zaps him with a "neuralyzer", a memory-erasing device from the Men in Black movies.
Mr. Burns says he got the idea to enclose Springfield in a dome from the Stephen King novel Under the Dome. Lenny makes a comment saying "It's already been done" referring to The Simpsons Movie. Mr. Burns even asks Smithers if he knew about it which he gives him a slow nod and a displeased look, since both he and him were in the movie at the time.
Nelson and Lisa's portrayal of the married couple is a reference to their past relationship. In fact, this episode is four episodes after "Loan-a Lisa", in which they apparently get back together. Another reference is made in a later episode, "The Great Simpsina", where Nelson threatens God that, "Ants will burn tonight!" if he doesn't bring Lisa back safe.
The music playing over the end credits is "Powerhouse", composed by Raymond Scott. The song is commonly heard in "assembly line" scenes in animated cartoons, particularly those made by Warner Brothers.
It had been mentioned before that Mr. Burns had multiple illnesses ("The Mansion Family") and that he was indestructible because the diseases canceled each other out. But another disease could have been developed that removed the balance. The man never said he was indestructible; just that the diseases he had canceled each other out.
When Lisa takes Mr. Burns to his mansion she says that she will show him that not everyone in Springfield is mean, despite Bart revealing that he was looking after Mr. Burns after finding him in the forest when he lost his memory.
When Akira is seen near the end of the line of patients outside the hospital, his hair is brown instead of the normal black.
However, Akira, just like anyone else, could have dyed his hair.
Mayor Quimby said about Mr. Burns "Give him what he wants. He's the only tax payer in this town." but we know this isn't really true. In the episode "The Joy of Sect" Mr. Smithers said that with their creative accounting, Mr. Burns only paid $3 per year. Also in "Papa Don't Leech" we know Mr. Burns is in the debt list for not paying his taxes but he was skipped by Mayor Quimby.
It could be possible, speaking of the latter episode and this one, that Mayor Quimby knew Mr. Burns didn't pay taxes and wanted to keep a secret in front of everyone.
Mayor Quimby said he thought Lisa was a midget but he has referred to her as a little girl numerous times before. This could possibly be a meta-reference to criticisms about the way Lisa is characterized, with many fans believing she is no longer characterized as a child.
At the barbecue party, Jimbo Jones insisted that his turn with Mr. Burns was at 2:00, just after Nelson's 1:30. However, according Homer and Bart's schedule, Jimbo was supposed to have his turn at 9:30, just after the Simpsons, and Nelson wasn't supposed to get his turn until 5:30. It could be that this was another day and a different schedule, however a scene with Snake at the Kwik-E-Mart approves the fact that he was supposed to get a turn with Mr. Burns after Apu, which would've been at 3:30.
In a rerun of this episode on November 28, 2010 on Sky1 in the UK, the scene where Otto uses Mr. Burns as a bong was cut.
Also, Lou states that they could just dig a way out if he did lower the dome. Ever since the movie was released, a very common question among Simpsons fans has been why no one in town thought of digging a way out from under the EPA's dome. It could have been that due to the army surrounding the dome, no one could dig themselves out without being caught.
When the Springfielders have their half-hour turns at taking revenge on Mr. Burns, a rota of name and times is seen. One of the names on it is Artie Ziff, revealing him to be still alive and apparently out of prison.