In Alvin and the Chipmunks, when Dave arrives home from work after finding out the Chipmunks drew on his presentation boards, the Chipmunks can be seen watching the episode, "Have You Seen This Snail?". The opening theme is also heard twice.
In the film Ted, Ted and John watch the episode "Procrastination" on TV while smoking marijuana.
In Zathura, Danny and Walter fight over watching SpongeBob and SportsCenter. The episode on the TV is "Bubblestand".
In the George Lopez episode "Why You Crying?", when George and Angie tell Benny that they punished Max by barring him from TV for a month, Benny quips "Wow, a whole month without the stupid talking sponge. That's gotta hurt."
The Two and a Half Men episode "Alan Hunter, Frontier Chiropractor" had Jake explaining the show's premise to his grandmother.
In the Yes, Dear episode, "Natural Born Delinquents", Kim tells Sammy that if he doesn't eat his vegetables, he will grow up to have arms like SpongeBob's. Later in the episode, as Greg tries to put Sammy to bed, a SpongeBob toy can be seen in Sammy's bedroom.
In a sketch on Sesame Street, Telly Monster's favorite Show Within a Show is revealed to be TriangleBob TrianglePants, featuring Bob as the title character, who sings a parody of SpongeBob's theme song. The name of the network the show airs on is called Triangleodeon.
In the second episode of the first season of Mario and Luigi's Stupid and Dumb Adventures, Mama Luigi sings the Krusty Krab Pizza song as he rides on a flying Mario's back. When Mario objects to him singing it, Mama Luigi refers to him as Squidward and himself as SpongeBob, because Mario's grumpy and he is happy.
In the second episode of the third season of Mario and Luigi's Stupid and Dumb Adventures, one of the dimensions Mario travels to is SpongeBob's dimension. Because it is underwater, Mario nearly drowns trying to grab the remote that sends him to other dimensions.
In part 3 of the "Chef Pee Pee Quits!" saga, Officers Goodman and Pee Pee find out from their police radio that a seven-year-old kid named Patrick Coleman ran away from his house when his mom wouldn't let him watch SpongeBob.
In The Stinger of "Bowser Junior's Halloween Problem!", Black Yoshi dresses up as SpongeBob for Halloween, and says, "I'm ready, I'm ready!" when Mario, who is dressed as Bowser, asks him if he's ready to go trick-or-treating with him.
In "Chef Pee Pee's Birthday Surprise!", Junior makes a bet with Cody that Chef Pee Pee will say, "Ravioli Ravioli, give me the formuli!" when he opens the skateboard that Joseph got him. Chef Pee Pee does just that, much to Cody's ire.
In "Substitute Teacher!", when Judy, as the substitute teacher, attempts to teach the class Marine Biology, she tells the class that little yellow sponges live in sea pineapples with their pet snails and their grumpy squid neighbors. Cody is not amused, and when Judy attempts to sing the SpongeBob theme song, Jeffy tosses a globe at her.
In "Jeffy's Tantrum!", Jeffy wants Mario to buy him a $2.99 SpongeBob game on the App store, which Mario refuses to do.
In "The Magical Button!", Junior finds a magical button that can grant any wish at the cost of killing a random person. At one point, Junior wishes for an ice cream truck (at the cost of killing Chef Pee Pee), and he gives Joseph and Cody SpongeBob popsicles from it.
In "Jeffy Gets Help!", Jeffy forces Mario to let him watch SpongeBob, and wears sunglasses of Patrick (whom he refers to as Squidward). In the episode he watches, Patrick is upset that he can't get a girlfriend, and SpongeBob tells him, "Well, I don't have holes for nothing!".
A live-action Parody Commercial features scrubbing product SpongeWow, who is used to clean up non-FDA approved hot sauce, much to his pain.
In The Simpsons episode "The Wife Aquatic", an exhibit on marine biology has a figure of SpongeBob.
The credits to "She Used to Be My Girl" have Lisa praying to God, Buddha and SpongeBob.
In a Treehouse of Horror episode, a bunch of movie monsters realized not many people are scared of them anymore, so they decide to dress up as popular characters from movies and TV shows. Frankenstein dressed up in a SpongeBob costume.
Another THOH episode listed director Bob Anderson as SpongeBob Anderson pants in the opening credits.
In "Yellow Stuberfudge", Lisa recommended to Krusty that he should make his show international, after seeing him broke. She then shows him an italian SpongeBob parody as an example. The parody featured SpongeBob giving Squidward a birthday present. Squidward tries to explain that the present is a mine from World War Two, before a seahorse sits on the activation button and blows the two up. A widowing fish shows up seeing what happened before letting out a Big NO!
In the Lego episode, Comic Book Guy mentions that Bart's mecha suit he made from the school was made of Batmobile, Hobbit Hole, and SpongeBob playsets. If you look carefully at the mecha suit, you can see parts of the Pineapple set.
In the My Little Pony: Friendship Is Magic episode "Sisterhooves Social", Sweetie Belle attempts to make breakfast and somehow burns the juice, ala Squidward burning a shake in "Pickles".
The Family Guy episode, "Road to the North Pole" has Stewie venturing to the North Pole to kill Santa. Brian tries to talk him out of it by explaining that Santa isn't real. In disbelief, Stewie asks, "Is SpongeBob not real?"
Phineas and Ferb had Phineas frantically looking for materials to get him and his friends off a desert island.
What's interesting is that co-creator Dan Provenmire worked on the show in the past as a writer.
The Drawn Together episode "Wooldoor Sockbat's Giggle-Wiggle Funny Tickle Non-Traditional Progressive Multicultural Roundtable!" had Princess Clara describe Wooldoor Sockbat's children's show as the gayest kid's show since SpongeBob. Additionally Wooldoor himself is an Expy of primarily SpongeBob.