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- This Best Buy advertisement from the early 90s.
- Brook's flashback in One Piece features all of his crewmates singing one final song before they all die. As they die one by one, Brook notes how the song ("Binks' Sake") dwindles down to a quartet, then a quintent, followed by a duet, and ending with a solo performed only by him, just like Old Fred does during the Blue Meanie assault. In the end, the pirate dies alone, leaving only the accompaniment to play.
- Astérix: In the French version fish monger Ordralfabetix' wife is called Ielosubmarine.
- The second volume of The League of Extraordinary Gentlemen featured "The Traveller's Almanac," which detailed all the places that Allan Quatermain and Mina Murray visited during a long absence from the League. One of the passages mentioned a brightly-colored phantom submarine and "a species of blue kobold found in Argentina."
Live Action TV
- Parodied in The Rutles: All You Need is Cash (with a clip from "Yellow Submarine Sandwich").
- In Homestuck, the Captor lusus is a "Bicyclops". To further cement the reference, their blood color is yellow.
- Futurama: Bender's Game features a parody of the movie with the Planet Express ship getting more "submarine-shaped".
- In the The Simpsons Last Exit To Springfield episode Lisa has a dream sequence under the influence of laughing gas, inspired by imagery from the movie, even with the Beatles passing by in a zeppelin, rather than a submarine. The same episode has a shot of part of Mr. Burns' mansion — a ridiculously long corridor studded with doors on both sides.
- The Batman: The Animated Series episode "What Is Reality?" features a hallway of Scooby-Dooby Doors like this film — in which one door opened by John precipitates a train roaring outward; likewise, when Batman opens a door labeled "Crazy Intent", a loco-motive roars out.
- The Powerpuff Girls episode "Meet the Beat-Alls" has two brief appearances by the Fab Four themselves: one with the character designs from this film, the other with the designs from their 1965 series. Sergeant Pepper from the Townsville police is based on Old Fred. And he requests assistance by quoting/paraphrasing the lyrics to Help!, much like Fred does in Yellow Submarine.
- The Super Jail episode "Don't Be A Negaton" features a shared hallucination that begins with visuals similar to the ones in the film (referenced with the Twins riding a Submarine-like thing) and then becomes something MUCH worse.
- There's also a similar scene in the episode "The Last Pack" in which The Warden gleefully starts chasing a butterfly in a psychedelic, Yellow Submarine style imagination sequence, even going so far as to include very Beatles-sounding music in the background.
- The episode "Best Friends Forever" shows that the jail has its own petting zoo full of creatures that all look like they came straight from the Sea of Monsters.
- The Teen Titans episodes featuring "Mad Mod", especially the second of the two, "Revolution", employ visuals that are a large-scale homage to this film.
- The Danger Mouse episode "The Dream Machine" has DM and Penfold inside Baron Greenback's dream cloud which has a series of doors with strange things emerging from them.
- The end credits sequence from Cloudy with a Chance of Meatballs is an homage to the film.
- In the first episode of the South Park "Imaginationland" trilogy, when the boys first go to Imaginationland, one of the imaginary creatures to greet them is a Blue Meanie.
- In the Muppet Babies episode, "Once Upon an Egg Timer", the babies take turns telling a story when Rowlf loses his voice. When Scooter has trouble telling a story, he turns it into a song, which the babies perform against a stylized, surreal, Yellow Submarine-esque backdrop.