Sideshow Bob's prison number in this episode is A113. A113 is a little known easter egg Brad Bird puts in his movies and films, such as this one, all the Pixar films, two other Simpsons episodes ("Krusty Gets Busted" and "Cape Feare"), and many other films and cartoons.
An alien appears in Hanger 18. This is a reference to the Roswell, NM UFO crash in the '40s, where it was said that the aliens and spaceship parts were held in Hanger 18 of the Wright-Patterson airforce base.
At one point, Milhouse plays with the cockpit of an F-15 and tries to act like he is blasting his mom, dad, and Sally Waxler out of rage that he had to be sent to a counselor. According to the DVD Commentary, this scene was what inspired them to create "A Milhouse Divided", the episode where his parents divorced.
The air show is on November 25th, and this episode aired on November 26.
This is the first episode to play the 20th Century Fox Television music in the background during an episode (In this case, the TCFTV music is heard while Sideshow Bob's prison mate is watching TV on his top bunk bed, causing Bob to have trouble sleeping).
When Chief Wiggum says "Where's that guy who eats people and takes their faces?", this is possibly a reference to the popular horror film series The Texas Chainsaw Massacre, specifically the way the film's main antagonist is a cannibal and wears his victims' faces as masks.
Homer flattens all his car tires by driving over a spike strip on a gate, the same way as in "Homer Loves Flanders".
After Sideshow Bob demands that all TV must go, Dr. Hibbert says, "Surely he doesn’t mean VH1".
While setting up the nuclear device, Sideshow Bob is whistling 'We'll Meet Again', a song used in the 1964 film, "Dr. Strangelove or How I Learned To Stop Worrying and Love The Bomb", a film about nuclear deterrence which ends in the world being destroyed by nuclear weapons. The "War Room" seen in this episode is also based on the one from that film.
Colonel Hapablap shouts "What is your major malfunction, Sideshow Bob?" a la Gunnery Sergeant Hartman (also played by R. Lee Ermey) in Full Metal Jacket.
The title of the episode is a pun on this line in “The Star-Spangled Banner”: “What so proudly we hailed at the twilight’s last gleaming.”
Professor Frink, during the war room scene, is drawn to resemble Dr. Strangelove. Complete with wheelchair.
After Sideshow Bob detonates the atom bomb, Maggie is seen plucking a flower as the camera zooms into her eye pupil, subsequently transitioning to a mushroom cloud. This sequence parallels Lyndon B. Johnson's infamous "Daisy Girl" ad from 1964.
Women could not serve in combat in the U.S. military until 2013.
Homer drinks six glasses of alcohol-free Duff, which are stated to cost $6 each. However, he is charged $48 instead of $36.
The Colonel is wearing a star on each shoulder, which is the insignia of a Brigadier General; a Colonel would have an eagle instead of a star.
When Sideshow Bob appears on the Tyranno-Vision to make his threat, the raise in his voice pitch due to the helium is noticeable. When he comes back on to point out the irony of his threat and when he's watching Springfield's TV stations go off the air, his voice is clearly normal. He could have been pushing it out of the way, similarly to when Lisa figures out where he is.
The "severe tire damage" sign is on the wrong side of the fence.
When Homer, Marge, and Lisa chase Sideshow Bob and Bart, Maggie is nowhere in sight. However, she is present when Bob is captured.
The computer terminal is in the blimp's airbag rather than in the gondola.
At the end of the chase scene (when Bart tries to jump onto the car), Marge's necklace appears to be white for a second.
Sometimes, when Sky One reruns the episode, the episode is mistakenly named as "S is for Sideshow Bob".