- Ringo and Fred pass through a room containing various pop-culture heroes, including John Steed, Mandrake The Magician and The Phantom. The latter also sort of a Mythology Gag as The Phantom, Mandrake and Yellow Submarine are copyrighted by King Features.
- Fred: Can't we take one of these?
Ringo: No, Fred, I only work with me mates.
- The Sea of Monsters segment includes a parody of the then-current Hamlet cigar TV commercials (hence the incorporation of "Air on a G String" into the music at that point).
- The line "It's a pair of kinky-boot beasts!" is a reference to the 1963 song "Kinky Boots", recorded by Patrick Macnee and Honor Blackman.
- In the Sea of Monsters, Old Fred presses a button, causing a load of miscellaneae to emerge from the sub. One of them is a banner that reads "The Rolling Sto-" before zipping back in.
- While the Beatles are quietly moving through the ranks of the Blue Meanies, Ringo sings, "tiptoe through the Meanies", a reference to an old song which was later covered by Tiny Tim.
- The second-in-command of the Blue Meanies is named Max (after the film The Blue Max.)
- Several Beatles songs that weren't used directly in the film get referenced:
- Fred: Won't you please, please help me? ("Help!")Jeremy: Enough to fill the Albert Hall. (As part of a string of references on "A Day in the Life", one being that The Sea of Holes reminded John of Blackburn, Lancashire, to which Paul replies sing-songedly, "Oh, boy!")Paul: Getting better all the time. ("Getting Better", obviously)Pepperland John: I'm the alter ego, man.
John: And I'm the ego man, goo goo g'joob. ("I Am the Walrus")Lord Mayor: (to Old Fred) No time for trivialities. ("When I Get Home")
John: The sub is taking off without us.George: You mean, 'within it, without us.'Paul: This is no time to plug one of your songs! (a nod to George's "Within You, Without You")
- In the Gold Key Comics adaptation as the sub takes off with the Beatles and Old Fred in pursuit:
Ringo: I've got a hole in my pocket!
- This is followed by an encounter and wooing of a meter maid named Rita. ("Lovely Rita")
- Then later, in the live action part:
George: A hole?
Ringo: Well, half a hole, anyway. I gave the rest to Jeremy!
George: What can he do with half a hole?
Paul: Fix it, to keep his mind from wondering! ("Fixing a Hole")
Paul: Hey, Ringo, you're not half the man you used to be. ("Yesterday")
- When the Beatles and Old Fred start to regress in age in the Sea Of Time:
- A couple of bars of "With A Little Help From My Friends" get played.
- The frightening orchestra crescendo from "A Day in the Life" gets used for the start of the submarine's journey home.
- In the opening sequence, when George is introduced, the opening of "Love You To" plays.
- When the Beatles arrive in Pepperland, in order to "un-bonk" the Lord Mayor the four loop part of the lyric of "Think For Yourself".
- When Ringo uses the hole in his pocket to break open the glass bowl imprisoning Sgt. Pepper's Lonely Hearts Club Band, the opening bars of "Baby, You're A Rich Man" play.
- In the original cut of the movie, the boys sing half of the first verse.
- George's catchphrase "It's all in the mind you know" is from The Goon Show (a suitable reference, as the Beatles really were fans of the Goons).
- John says this a year earlier in The Beatles episode "Strawberry Fields."
- The Apple Bonkers' Weapon of Choice look like the logo of a certain record company.
- After the boys sing life back into Pepperland, the Chief croaks, "Hark...the hills are alive..." with Max replying in sing-song, "With the sound of music..."
- The Boob, after he fixes the Sub's motor, quips "I must complete my bust, two novels, finish my blueprints, begin my Beguine." The last part refers to "Begin The Beguine," a 1935 song composed by Cole Porter.
Shout Out / Yellow Submarine
Yellow Submarine has many Shout Outs within the film, and there are many references to it in other works. See the Referenced By page for the latter.