In part one of the first season finale of the 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.
Marvin's host father was bitten by an alien, and started hallucinating, he then held up an umbrella and said "Here's your clarinet Squidward."
In the ABC cartoon The Weekenders, there was a rock band called the "Chum Bukkit", which is probably a reference to the Chum Bucket.
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.
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 molluscs photos.
In "Treehouse of Horror XX", a Frankenstein's monster was dressed in a SpongeBob costume. Later, SpongeBob told the Simpsons he was secretly very evil.
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. And 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 and says that the gift is a mine from World War II. Then, a seahorse presses the button which makes that the mine explodes and kills Spugna Roberto & Squiduardo in pieces. Then, a fish appears and says: "Calamari?", screams: "No...!" and starts crying. In the parody, Roberto lived in a watermelon under the sea. Actually, SpongeBob lives in a pineapple also under the sea in the original TV animated series from real world..
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 their diets 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 were real and asked if Squidward really gives SpongeBob the business.
What's In the Bible
In the 4th JellyTelly DVD, Michel mentions his brother was wearing some SpongeBob underpants & later calls him "Mr. SpongeBob UnderPants".
In "Finns of War", a sea sponge who looks like SpongeBob is seen.
Wooldoor Sockbat is a parody of SpongeBob, spoofed also with Stimpy (from The Ren & Stimpy Show) and the Looney Tunes characters, also he has a theme music Similar to Spongebob's
In the Dvd version of Captain Girl episode, between Toot Jumping through the water and Toot inside it, the narrator says "Three Weeks later", then it shows the island of Spongebob, with the Drawn together house between the Palm trees.
In Tell My Mom, Sandy gets pregnant and SpongeBob realizes she used him to protect her.
In Major League of Extraordinary Gentlemen, SpongeBob discovers Mr. Krabs' secret formula. Krabby Patties are made from crabs.
In That Hurts Me, a sponge and a starfish dance with eachother, barf, and then dance with eachother again. The characters in this resemble SpongeBob and Patrick.
An episode spoofed SpongeBob as "TriangleBob TrianglePants" which was Telly Monster's favorite show. The show starred a triangle man version of SpongeBob.
In an episode, Oggy is seen hiding in the mailbox and pops out to receive his mail, which is similar to how SpongeBob scares the mailman in the episode "Chocolate with Nuts".
In another episode, "Run, Olivia, Run", one of the spectators was wearing a SpongeBob costume.
King of the Hill
In the episode Tears of an Inflatable Crowd, Kahn mentions SpongeBob when he wants to create an diversion. Hank and Peggy look at him oddly while Kahn replies "I don't know what kids like".
The Cleveland Show
Early in the episode Buried Pleasure, Cleveland has holding a banana-shaped stuffed toy that looked like SpongeBob.
In another episode, Holt mentions SpongeBob.
Fanboy and Chum Chum
In the episode, "Cold War", Kyle gets chased by Fanboy and Chum Chum clones in a similar way to the robot chasing the man in the episode "Krab Borg". Yet, the episode has a similar plot to "Naughty Nautical Neighbors", and when Kyle enters the fanlair, it's similar to how Squidward enters SpongeBob's house in "Pineapple Fever".
The episode "Excuse Me" has a somewhat similar plot to "Ditchin'".
In the episode "A Smith in the Hand", after Stan announced his new station Clean TV, in one scene, several kids can be seen crying to their mother with one of them saying "Where's SpongeBob" and another saying "I want Patrick!".
In a commercial for Instant Mom, the lady plays a game where you tell if it is real or fake and asks,"Is SpongeBob real?"
The Adventures of Jimmy Neutron: Boy Genius
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 faint light can be seen at the mid-right. A commercial stated that the light was SpongeBob's pineapple.
America's Funniest Home Videos
In one episode a guy in a SpongeBob cosume was shown running around in circles and then he falls. Tom Burgeron calls him "SpongeBob ClumsyPants"
In another episode a SpongeBob birthday cake is seen.
In another episode there was a boy picking his nose who was wearing a SpongeBob T-shirt.
Pretty Little Liars
In one episode, when Hanna is talking to Mona, she mentions SpongeBob & Patrick.
The Creative Pet Grooming Show 2013
When a women walks into a room the SpongeBob theme can be heard.
In one episode, SpongeBob appears only he was green instead of yellow.
In another episode, SpongeBob was seen in the background several times.
Sam and Cat
In the episode #TextingCompetion when Cat was mentioning what could do with the speed boat she said number 3 look for Spongebob's pineapple!
Not Going Out
In an episode of Not Going Out, Tim mentions SpongeBob SquarePants.