One of the Asian gang members in the Russian roulette game looks like Richard Sakai, a producer of The Simpsons.
This episode reveals that Homer posed for two pictures that only two people know about: the pin-up that Barney hangs in the barracks during basic training and the file photo of Homer dressed as a Russian and holding a bottle of vodka (which Lisa knows about, as she warned Homer that the photo will come back to haunt him).
A portion of the song "In the Navy" is played in this episode 1.1 times faster than in the original music video. Waylon Smithers can also be seen dancing there at one point.
The five Naval officers who were unable to indict Homer due to their own problems had the following reasons:
Homer has a dishonorable discharge from the Navy, despite that he was never really indicted (as everyone else in the Navy had their own crimes and he was let off the hook).
In reality, a dishonorable discharge can only be given by a General court-martial (comprised of five officers), and is equivalent to a felony conviction.
Also, there are five officers in the tribunal hearing, yet only four admit their reasoning as to why they can't indict Homer due to also being indicted for their own problems. A fifth, a woman, was part of the hearing and was animated, but her bit was cut from the final episode in its entirety & was not part of the Season 9 deleted scenes, so her reasoning is unknown.
The moustachioed bald officer when it shows the tribunal shows him with his hat on the officer's podium. But when it cuts to his leaving and his giving his reasons for not indicting Homer, it is instead replaced with a blonde wig.
Homer states that the Naval Reserve is not allowed to fire at anyone but Greenpeace, but Homer ordered someone to fire a torpedo at an enemy sub.
The ship Homer was supposed to tie to the docks (that ends up sailing away and plunging down a waterfall) is actually big enough to drop anchor.
The lead singer of The Village People (the police officer) is yellow ("white") on the show. In real life, he's black.
When Homer and Lisa watch the Naval recruitment advert, Lisa is initially shown in her nightgown, in the next shot of Homer and Lisa, Lisa is wearing her civilian clothes.
“Fear of Flying“ and "Mother Simpson“: Smithers listens to a song that is commonly associated with gay men ("It's Raining Men" by The Weather Girls; "Waterloo" by ABBA; and "In the Navy" by The Village People).
The opening couch gag is a recreation of the Rocky and Bullwinkle animated bumper seen at the end of each Bullwinkle short. The music accompanying it is also adapted from the original music in the bumper.
Many parts of the episode, including the title, refer to the 1995 film Crimson Tide.
The character Captain Tenille is based on Captain Frank Ramsey, a character in the film who was portrayed by Gene Hackman.
This episode shows the Russian ambassador in the U.N. stating that the Soviet Union's breakup was "what we wanted you to think." This is followed by the showing of several floats in a Moscow Parade being destroyed to reveal several tanks underneath to take their place, the Berlin Wall coming out of the earth and Lenin being unfrozen. During the revelation sequence, a portion from the song Prince Igor, Act I, Scene 1: Chorus is played.
In the scene where Homer is trying to sign up for the Naval Reserve, he questions an officer about a question that was scratched out. This was a reference to the Don't Ask, Don't Tell policy that Bill Clinton proposed where he would allow gays in the Armed Forces, as long as they were not openly gay in the military. Consequently, the Armed Forces were no longer allowed to "ask" soldiers if they were gay (hence the question now being crossed out and the officer trying to avoid hearing Homer answer the question.)
One of the officers who refused to indict Homer stated that it was because he was indicted for impersonating the First Lady and was seen leaving with a blonde wig. At the time the episode aired, Hillary Clinton had been the First Lady in question.