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In the episode "Operation: Rescue Jet Fusion," Jimmy, Carl, and Sheen go into the ocean to look for a tracking device, and when they find it, a pineapple can be seen at the mid-right. A Nick Extra Close Look stated that the pineapple was SpongeBob's house.
In one episode named "The Last Last One Forever and Ever," a live-action episode, Meatwad (who is portrayed as a yoga ball) is helping Master Shake (who is portrayed as a human named "Don Shake") write a story, and suggests writing a story about "A sponge who lives in a pineapple under the sea." Shake says "Hasn't that already been done?" and Meatwad replies "No. I don't think so."
In the episode "Shake Like Me," Meatwad says he wants a SpongeBob bounce house.
In part one of the first-season finale, Master Pakku coyly stated to one of his students, "Nice work... a couple more years and you might be ready to fight a sea sponge." The show's creators later said in the audio commentary of Siege of the North Part I that his statement was a friendly poke at SpongeBob SquarePants.
In the episode, "The Earworm Reverberation," Sheldon is trying to think of a song that he can't remember, so he's trying to guess songs off the top of his head, and one of the songs he thinks about is the "SpongeBob SquarePants Theme Song," and even sings the first line.
In the episode, "The Justice League Recombination," Zack says "Turns out that if you kill a starfish it'll just come back to life.", to which Sheldon replies, "Was the starfish wearing boxer shorts? Because you might have been watching Nickelodeon." It's a reference to Patrick Star and the shorts he wears.
In the episode "The Separation Oscillation," Howard says "I'd like to SpongeBob her SquarePants."
In the episode, "The Locomotion Reverberation," Raj and Stuart are left to watch Halley, who is Howard and Bernadette's baby daughter. After talking on the phone with them and hearing how incompetent they seem, Bernadette moans "I may have just left my infant daughter with Patrick and SpongeBob."
In the episode "The Long Distance Dissonance," Sheldon can be seen watching the episode "Plankton!" on his phone.
Ironically, both Sheldon Cooper and Plankton both share the same first name, that name being 'Sheldon.'
In the episode "Thursday" a poster of SpongeBob's face can be seen hanging on the wall in Josie Trent's and Corrine Baxter's dorm on Josie's side of the room. It is most noticeable during the scene where Josie is dancing to her radio.
In Season 3, Episode 11 (Episode 22 in Australia), before Team Venom opens up the barrel to reveal the luxury they won in the Captain's Challenge (being ice-cream) Asad Karim (who was captain and was the one chosen for the task) recites the opening lyrics from the theme song.
In "Wish Fixers," Timmy wishes to have running pants made of cheese, and then Cosmo calls Timmy "CheeseBoy SquarePants."
Another reference can be found in the episode, "Something's Fishy," where the king of Atlantis, Greg, states that the diets of the merpeople consist of "crabs, starfish, and the occasional underwater squirrel," as a joke to their fellow Nick animators.
Another reference can be found in the episode "App Trap" where the first kid with the smart phone has SpongeBob's pants, buck teeth, eyes, hair, and freckles.
In "Road to the North Pole," Stewie asks Brian if SpongeBob and Elmo are real and asks if SpongeBob really gives Squidward the business.
In "Turkey Guys," a balloon of a SpongeBob parody called "SpongeCow" is seen during a Thanksgiving parade.
In "Inside Family Guy," when Peter is doing a job as a Hollywood Boulevard mascot before deciding to return to the show, a person in a poorly made SpongeBob costume can be seen taking photos with tourists. In real life, there is a SpongeBob mascot on Hollywood Boulevard.
In "World of Emma," Emma ended up wishing for Adil to make Sophie more like her. After he did, Sophie asked Emma if she had any pink nail varnish. Emma then replied with "Does SpongeBob have SquarePants?"
In the episode "King of the Castle," Fee is shown holding a pizza box with the words "Pizza Castle" on it. Patrick mentions a restaurant of the same name in "The Bully," which was written by C.H. Greenblatt, creator of Harvey Beaks.
In the episode "Secret Gordon," if one looks closely in the garden right before it closes up, there is a hedge shaped like SpongeBob.
When Fee is showing Foo the baby mobile she made for him in "Fee's Pyramid", there is a snail on the the mobile that slightly resembles Gary.
In the episode "House of Cameras/House of Numbers," Victor tried installing video cameras in order to try and keep a close eye on the students living in the Anubis house. While trying to get rid of the cameras, Nina mentioned that they needed help from their house's comedic duo. Although she meant Alfie and Jerome, Amber thought she was talking about "SpongeBob and Patrick."
In the episode "House of Crushes/House of Vertigo," Poppy asked Mara about what her dad's like. One of the things that Mara mentions is that he "dances like SpongeBob."
In the episode "Left in the Dark," SpongeBob and Patrick can be briefly seen on the television.
In the episodes "Making the Grade," and "Friend or Faux?," a poster in Lisa's kindergarten class shows characters from the show: a red crab (Mr. Krabs), a yellow sponge (SpongeBob), a pink starfish (Patrick), and a blue octopus (Squidward).
SpongeBob was parodied in some segments of this Cartoon Network series during its three-year run:
Opening: A clay-animated character resembling SpongeBob is shown.
"Celebrity Birthdays" - Mort Jenkins, a jellyfish who landed the role of Jellyfish #56 on SpongeBob SquarePants, is one of the celebrities whom's birthday is being celebrated.
"WALL·E·NATOR" - The WALL·E·NATOR squeezes a round SpongeBob (who has eaten too many Krabby Patties) back into a square.
"Cliffordfield" - The Sesame Street character Big Bird gets squashed into SpongeBob by a rampaging Clifford the Big Red Dog, disproving his statement that he's "a one-of-a-kind children's character."
"Who Wore it Better?" - In this sketch, SpongeBob is one of the candidates among various others, who are being debated on who wore a white sundress best.
"MAD vs. Wild" - Bear Grylls, attempting to survive in the wild, plucks Gary from a tree stump and eats him, although regretting that he ate him while he still had his shell.
"Celebrities Without Their Makeup"- SpongeBob, dressed like an elf, is depicted as a fruitcake when seen without his makeup.
"¡AY Carly!" - A Mexican version of SpongeBob, named "SpongeRoberto SquarePants," is shown at the end of the sketch.
"Law & Ogre" - A framed picture of SpongeBob is seen at the Big Bad Wolfgangbucks restaurant.
"Pirates of the Pair of Tweens" - Plankton goes "planking" with Captain Jack Sparrow on the roof of the "Crabby Crust."
"SpongeWOW" - SpongeBob is seen as SpongeWOW, a parody of the ShamWOW towel, in this infomercial spoof. He is used by a spoof of Vince Offer to wipe up various spills against his will, including twelve bottles of non-FDA-approved hot sauce, which leaves his face burning, and he even says, "Kill me now!"
"Abs-Duction" - Actor Taylor Lautner goes to Mr. Krabs' house, thinking he is his real father. Mr. Krabs responds by slamming the door at him, angrily.
"New Gill" - Ariel from The Little Mermaid tries to find a new boyfriend after being dumped by Prince Eric for Ursula, and ends up dating SpongeBob, who she finds to be too chipper for her.
"iChronicle" - SpongeBob and Patrick can be seen on a Nickelodeon blimp.
"Fart or Chair" - In this game show spoof, SpongeBob is seen sitting in a massage chair.
"The Blunder Games" - A SpongeBob balloon is seen at a parade (in a parody of the 2012 film The Hunger Games).
"Taking Nemo" - SpongeBob is interrogated by a furious Liam Neeson on the whereabouts of Nemo (from Disney/Pixar's film Finding Nemo).
"Dark Knight at the Museum" - SpongeBob is seen shouting "I'M READY!"
"SpongeBorg SquarePants" - In this sketch, SpongeBob is a cyborg that turns the inhabitants of Bikini Bottom into cyborgs.
"Doraline" - Plush toys of SpongeBob can be seen at the Cheap Knock-Off Stand.
A Glorp Corp Mixel named Glorp voiced by Tom Kenny in "Nixel, Nixel, Go Away" reverses the effects of the zombification of his town's citizens by the main antagonist, all through the power of song similar to SpongeBob (also voiced by Kenny) in "The SpongeBob SquarePants Movie."
In the episode "Nicky, Ricky, Dicky & Dawn Go to Hollywood," a SpongeBob statue made with LEGO bricks can be seen in a scene when Anne Harper poses with the statue, and impressions the SpongeBob laugh.
In the pilot episode there is a cameo of an identical character to SpongeBob appearing at a nightclub between the characters. The character even makes it clear that is not SpongeBob, but a cheese while chatting with a female bread.
In the episode "The Old-Fashioned Sunday", Karen was annoyed at Pete for turning the TV off because she wanted to watch SpongeBob SquarePants and claimed that it shows how to make Krabby Patties and states about what happens under the sea, which Pete didn't listen to as he said about there being lots of programmes about what goes on under the sea.
In "Phineas and Ferb-Busters," Doofenshmirtz runs away from a robot similarly to the guy in the scary robot movie from "Krab Borg." Also, Doofenshmirtz and the guy being chased by the robot are both portrayed by Dan Povenmire, who was also a writer, storyboard artist, and storyboard director on SpongeBob, meaning this reference pretty much comes full circle.
In "Summer Belongs to You," Phineas finds a sponge and a starfish while digging a hole on a deserted island, a reference to SpongeBob and Patrick.
In one episode, at the end it can be seen a boy that looks like very similar to SpongeBob with yellow hair, a square-shaped head, blue eyes, two teeth, and also wearing a shirt with a red tie and brown short pants, with the expection that the shirt that used the boy is blue.
In That Hurts Me, a sponge and a starfish dance with each other, then run out of energy. They crawl offscreen, exhausted, and then they can be heard snorting cocaine, and then the two run back on screen with high energy and dance with each other again. The characters in this sketch resemble SpongeBob and Patrick.
In Tell My Mom, Sandy gets pregnant and SpongeBob realizes she used himself (a sponge) to protect her.
In Major League of Extraordinary Gentlemen, SpongeBob discovers Mr. Krabs' secret formula for Krabby Patties and reveals it to the patrons of the Krusty Krab: they are made from crab meat. He also points out to Squidward that the calamari rings he is eating are actually made from squid (while oddly, Squidward is an octopus), and informs a customer that her "Chicken of the Sea" salad is made with tuna. An angry mob of customers approach Mr. Krabs and attack him. SpongeBob then says that he's glad nothing disgusting ever happens to a sponge, and the scene cuts to a nurse informing a morbidly obese patient that she will be scrubbing deep within his rolls of fat with a sponge, and his examination will then be over. SpongeBob then pushes the scene aside, reiterating, "Nothing disgusting ever happens to a sponge!" A squish is then heard from the other scene, and the nurse says, "I hope that's pudding in there."
An episode spoofed SpongeBob as "TriangleBob TrianglePants" which was Telly Monster's favorite show. The show starred human cast member Bob, as a triangle man version of SpongeBob.
As an effort to help spread diversity in society amongst elementary school age children, the "We are Family Foundation" made a music video of the popular disco song of the same name, with multiple characters from shows on Nickelodeon, Disney Channel, and PBS Kids. The Sesame Street muppets were used heavily in the video, while clips from "Bubblestand" and "Jellyfish Jam" were shown throughout. However, since the company sponsoring the video got confused for a similarly named company that promoted same sex marriage, the media interpreted a rumor that SpongeBob and Patrick are a gay couple.
In "She Used to Be My Girl," Lisa, needing a god to pray to, tells a newscaster she is praying to Jesus, Buddha, and SpongeBob. Then the camera shows heaven, where Jesus, Buddha, and crudely drawn SpongeBob are. Buddha asks Jesus, "Perhaps we should help?" and SpongeBob interrupts, saying "Screw her!," then laughs insanely, while Jesus shakes his head.
In "The Wife Aquatic," Marge and Lisa go to an aquatic museum where there is an exhibit that reads "The Science of SpongeBob" and it shows a SpongeBob statue next to it. Patrick Star also appears as one of the mollusk photos.
In "Angry Dad: The Movie," Bart mentions SpongeBob when he claims he likes cartoons. He says: "I've always loved cartoons, going way back to the real early SpongeBobs."
In "Yellow Subterfuge," When Krusty asks to Lisa if could sell foreign rights to your show, Lisa says that even SpongeBob did it. She shows him an Italian parodied version of SpongeBob SquarePants on her tablet called Spugna Roberto Quadrati Pantaloni ("Sponge Roberto Square Pants"). In the show, Spugna Roberto (a parody of SpongeBob SquarePants) gives a gift to Squiduardo Calamari (a parody of Squidward Tentacles) for his birthday; the gift is a landmine from World War II. Squiduardo declines the gift, and while he is talking, a non-anthropomorphic seahorse lands on the landmine's button, detonating it and blowing Spugna Roberto & Squiduardo to pieces. A fish arrives at the scene and exclaims "Calamari?, Noooo...!!!" and starts crying. In the parody, Roberto lived in a watermelon under the sea, spoofing SpongeBob's pineapple house.
At the end of the episode "Close Encounters of the Furred Kind", Sooty peeks out of the door and winks to the audience is similar how SpongeBob thumbs up and winks to the audience at the end of "Mermaid Man and Barnacle Boy."
In the episode, The Beast of Sodor, every time an engine or other character mentions "the abominable snowman," Dramatic Impact 2 plays, except in the beginning of the episode. But it was heard one more time when Sir Topham Hatt hears that Dowager Hatt called him the abominable controller when she was on Thomas.
There is a SpongeBob theme in the Mini collection.
In the episode "Alan Harper, Frontier Chiropractor," Jake explains the series to Evelyn, to which she replies "So bottom line...he's a sponge?" This clip was shown in Square Roots: the Story of SpongeBob SquarePants.
In "Like No Other Market on Earth" Equimorph morphs into a copyright friendly version of SpongeBob SquarePants known as "SpongeRobert RectangleShorts" who was voiced by Tom Kenny, SpongeBob's voice actor.
An episode of The X Presidents (from "TV Funhouse" on Saturday Night Live) depicts SpongeBob refusing to star in a pro-Gulf War II propaganda commercial, and getting held prisoner for it. Tom Kenny provides SpongeBob's voice, which is surprising as this clip has relatively adult content.