- Mermaid Man and Barnacle Boy reference both the Batman TV series and Aquaman and Aqualad. Man Ray is based off of Black Manta (and bizarrely shares a name with a surrealist artist).
- In "Mermaid Man and Barnacle Boy II", the retired supervillain Atomic Flounder unleashes an atomic breath on Barnacle Boy after getting annoyed by Spongebob, just like that of Godzilla.
- In "Sleepy Time", SpongeBob tells Gary "Mind your wandering eye, you little mollusk!", a direct reference to a lyric from the title track of Ween's album The Mollusk.
- In "Graveyard Shift", the flickering lights end up being caused by...Orlok? SpongeBob, Squidward and the "Slasher" just laugh it off. "Nosferatu!"
- From that same episode, when Squidward observes the creepy occurrences in the Krusty Krab, he ends with: "And the walls will ooze green slime! ... Oh wait, they always do that."
- Mr. Krabs (shouting in response to Sandy about why there's only one fast-food restaurant in Bikini Bottom) "...There can be only one, drylander!" (Mr. Krabs is Clancy Brown, who played The Kurgan in Highlander).
- Jürgen Kluckert, Krabs' German voice actor, gets his own Actor Allusion. In "Born Again Krabs", when faced with the Flying Dutchman, he calls himself "Benjamin Blümchen", a reference to the beloved German children's character that he had succeeded from the late Edgar Ott.
- The World's Smallest Violin in "Squilliam Returns" is a reference to a scene in, of all films, Reservoir Dogs.
- In "Pranks A Lot", Mr. Krabs says "I ain't afraid of no ghosts!"
- In the episode "Ghost Host", after the Flying Dutchman's failed attempt to scare SpongeBob, he takes the form of a horrible, worm-like monster with the head of J. R. "Bob" Dobbs, complete with pipe.
- "Spy Buddies" has a reference to the famous James Bond gun barrel sequence.
- In "Stanley S. SquarePants", it was revealed that Mr. Krabs has three nephews who solve mysteries.
- "SpongeBob's Last Stand" features a song called "Give Jellyfish Fields A Chance", which is a parody of John Lennon's "Give Peace A Chance". The scene that the song plays over is a parody of the music video for "Subterranean Homesick Blues".
- The middle of the jellyfishing song has a slight rewrite of The Toyes' Smoke Two Joints (replace "two joints" with "jellyfishing").
- "Wormsign!" *Cue a shot of a picket sign reading "Worm".*
- In "Rule of Dumb", "With great power comes great responsibility."
- In the episode "Sailor Mouth", there is a shoutout to George Carlin's Seven Dirty Words routine in this exchange:Mr Krabs: There are 13 bad words you should never use.
Squidward: Don't you mean there're only seven?
Mr Krabs: Not if you're a sailor. (chuckles)
- In "Christmas Who?", when Squidward (dressed as Santa Clause) asks a little girl what she wants for Christmas, she replies "Front teeth." This is a reference to the 1948 song All I Want for Christmas Is My Two Front Teeth by Donald Yetter Gardner.
- In "New Student Starfish", Patrick's climb up the mountain of light bulbs has a brief shout out to The Price Is Right's Cliff Hanger Game, complete with yodeling and lederhosen.
- In "The Camping Episode", Spongebob and Patrick end up smashing a guitar and a drum set, respectively. Okay, quite a few Rockers Smash Guitars, so that could be a Shout-Out to any of those bands, right? Fast forward to the episode "Sweet And Sour Squid" where Squidward and Plankton are clearly singing a parody of "Pinball Wizard", and it seems to indicate that at least one writer among the crew is a fan of The Who, meaning that in the Camping Episode Spongebob and Patrick were most likely imitating Pete Townshend and Keith Moon, respectively.
- During the tenth anniversary special, Robin Williams asked Patchy if he knew Captain Hook. Granted, this is Robin Williams we're talking about, so that line was likely to have been ad-libbed, but still...
- In "Squidbob Tentaclepants," Sandy's teleportation device bears a striking resemblance to Brundle's telepods.
- "Bye Squidward! Bye Mr. Krabs! Bye, Squidward." "You said "Bye, Squidward" twice." "I like Squidward."
- In "Hooky", when Patrick is riding on a hook like a horse, he shouts, "Heigh-ho, Silverfish! Away!"
- "Karate Island" is one long shout out to Game of Death, complete with Sandy wearing the famous yellow tracksuit Bruce Lee wore in said movie.
- The second half of "Squeaky Boots" parodies Poe's "The Tell-Tale Heart", where Mr. Krabs steals the rubber boots he gave to Spongebob and hides them under the floorboards of the Krusty Krab, only to still be driven mad by the squeaking.
- At the end of "Fear of a Krabby Patty":Giant Krabby Patty: Just remember, Spongebob, I'll always be with you right here. (points to a part of Spongebob's stomach with a glowing finger)SpongeBob: In my heart?
Giant Krabby Patty: Actually, in your arteries.
- In one episode, Mr. Krabs enters Sandy's dome for the first time and remarks, "It seems so much bigger once you're inside..." Sandy casually responds, "Yeah, that's what they all say."
- In "Hocus Pocus", Mr. Magic lives on a brown-tiled road.
- In fact Mr. Magic himself more or less serves the same role as the titular "wizard."
- "Plankton!"Plankton: You weak-minded fool!
- In "Pizza Delivery", Spongebob is called "Jethro" twice.
- "SpongeBob B.C." has the weird chanting and famous music from 2001: A Space Odyssey when prehistoric SpongeBob discovers that he can use fire to cook food.
- Another subtle reference to 2001 occurs in the episode "Sandy's Rocket", where a copy of the novel version can be seen floating in the rocket as Spongebob and Patrick briefly travel through space.
- Krabs Vs. Plankton: When Plankton enters the courtroom, the theme from The People's Court plays. No, not a Suspiciously Similar Song, the actual music.
- There is an episode called Krabby Road. Three guesses on what that's a pun of.
- This shout out was also in a Christmas short called Plankton's Holiday Hits, so this is basically a shout out of a shout out.
- Atlantis SquarePantis: The citizens of Atlantis resemble the Blue Meanie with Mark Chang's brain dome.
- In "Face Freeze", Spongebob and Patrick make a number of ridiculous faces that are just plain creepy. One of the ones Patrick chose to make? A... um... pink monstrosity with square ears, a pointed head, a menacing grin, and sunken-in black eyes... He would be the kind of person to turn the population into chocolate if he could, but isn't that going a little far even for him?
- In "The Bully", the scene where Flats chases SpongeBob down with a garbage truck is very similar to the climax of Back to the Future Part II where Biff chases Marty down a tunnel in his car - both Biff and Flats are even shown close up and laughing evilly behind the wheel. This would also be a very nice Actor Allusion, as Tom Wilson played both of them.
- In "To Save A Squirrel", Sandy uses the phrase "Eat or be eaten" to describe was survival training camp is like.
- "Big Pink Loser" has a shout-out to The Adventures of Buckaroo Banzai Across the 8th Dimension, of all things, when Patrick claims that his life's dream is "to defeat the giant Monkey Man and save the ninth dimension", later amending it to "to defeat the little Monkey Man and save the eighth dimension" when SpongeBob convinces him that it might be too hard. The titular "eighth dimension" was a key part of the plot of Buckaroo Banzai, and it also featured a race of villainous aliens who called all humans "Monkey Boy" ("It's not my goddamn planet! Understand, Monkey Boy?").
- In "Tutor Sauce", Spongebob accidentally sends Mr. Krabs flying into the background coral due to his reckless driving. Ed, Edd n Eddy fans might think of a similarnote gag in the episode 1 + 1 = Ed in which Ed interacts with the background houses.
- From "Missing Identity" after SpongeBob's "BLEEUGH!" (after trying Gary's Snailpo) reaches the Snailpo factory's offices:Female employee: What is it, Peterson?
Peterson: I'm not sure. I feel... a disturbance!
- One episode even had one in the form of a Running Gag.
- The premise of "A Pal For Gary", where Puffy Fluffy is bought from a gypsy and becomes a monster overnight, is modeled after the plot of Gremlins, where an adorable creature becomes a ravaging beast if fed after midnight. Only in this plot, the buyer ignores the seller.
- "This Grill is Not a Home", SpongeBob and Mr. Krabs' Distant Duet from "Welcome to the Chum Bucket", appears to be an Affectionate Parody of "Somewhere Out There".
- "Clams" has numerous references to Jaws, including the famous theme.
- There's also a reference to Moby-Dick, when Mr. Krabs nails a sandwich to the boat's flagpole as a reward.
- There's also a Jaws reference in "SpongeBob, Sandy, and the Worm," where the citizens are discussing what to do about the titular worm, when an old man who resembles a sailor scratches the wall in the same way the man in Jaws scratched the chalkboard to get everyone's attention. However, he just wanted to know where the bathroom was.
- In "Ditchin'", the new Mermaid Man and Barnacle Boy comic book includes a panel about their origin story, which has their parents launching them in a rocket.
- Using "Because they're so darn stupid" as the punchline to a lightbulb joke like SpongeBob does in "Squirrel Jokes" was previously done in Raising Arizona.
- At the end of "SpongeHenge", SpongeBob sees the Krusty Krab abandoned and half-buried in the sand and breaks down, a la the ending of Planet of the Apes (1968). His hair and beard make him look like Charlton Heston as well.
- To Larry "Lonesome" Rhodes' speech in A Face in the Crowd in "Chum Bucket Supreme", when Patrick resigns from slogan writing because his brain is burned out and Plankton boasts about the customers' gullibility:Patrick: Anyway, you can send my check to my home.
Plankton [unaware that his words are being broadcast over the loudspeaker]: Check? You want money for those stupid catchphrases? Anybody can sell to my idiot customers! They're buffoons, morons! They'll buy anything I sell them! They're the dumbest of the dumb, the stupidest of the stupid! They're dummies, dweebs, and doo-doo dunderheads. I can keep that rabble right where I want them! Huh? [A bunch of hockey players gang up against Plankton, and start hitting him with their hockey sticks]
- In "Fiasco!" Plankton ducks inside a movie theater to evade the cops for stealing a priceless art piece made out of a krabby patty. The movie shown is blatantly The Blue Lagoon complete with the two teen characters about to kiss.
- In the episode "Spy Buddies", Mr. Krabs and Plankton switched lives to settle a bet, where Mr. Krabs could steal the formula, and Plankton would fail to protect it. At the end, Mr. Krabs wins by stealing the formula, and the bet it settled by having Plankton pay Krabs "one a-dollar."
- "Spin the Bottle" has this quote by SpongeBob: "Friendship is magical, too."
- "No Pictures Please" opens with "The Tidal Zone", a reference to the The Twilight Zone (1959). It returns at the end after the tourist is revealed to have never existed in the first place. "The Night Patty" also ends with all the weird events that occurred being the Tidal Zone's doing.
- It can also be a reference to an early Hillenburg comic featuring a very early version of SpongeBob called The Intertidal Zone.
- In Pineapple Invasion, after challenging Gary to a fight, Plankton says, Put em up, put em up!
- "Feral Friends" features a green orb rising from a volcano and mutating everybody except Sandy into more savage, animalistic versions of themselves. It even has musical themes similar to the orchestral score in Heavy Metal.
- When the tough guy in "No Weenies Allowed" says he ate a bowl of nails for breakfast this morning without any milk, it is a parody one of Mr. Ratburn's secrets during the Arthur episode "Arthur And The Real Mr. Ratburn," as per Prunella's dialogue to the gang: "He eats nails for breakfast without milk!"
- One of the famous Mermaid Man and Barnacle Boy episodes is titled "Back to the Past", whose conflict revolves around trying to undo a Bad Future dominated by the Big Bad; Gee, doesn't THAT sound familiar to you?
Shout Out / SpongeBob SquarePants