Penny appears in a 90s spot for the Partnership For A Drug Free America, talking about why it's harmful for kids to do drugs, including that it can negatively impact one's body and brain, and get them in trouble at school or with the law.
In "Our Very First Show", Joey briefly impersonates Pee-Wee Herman to try to cheer baby Michelle up.
In "The Seven Month Itch: Part One", Uncle Jesse says that he's living in Pee-wee's Playhouse.
In "Mad Money", Danny compares Joey to Pee-Wee Herman, saying he's a grown man who still watches children's cartoons. Joey then does an impression of Pee-Wee, telling Danny "Sticks and Stones may break my bones, but names will never hurt me."
Jesse: How would you like to be watching, when suddenly, (imitating Elvis) "You ain't nothin' but a hound dog" (imitating Pee-Wee) "I know you are, but what am I?"
Pee-wee and Chairy appear in the celebrity version of "Put Down the Duckie".
In Episode 3075, The Amazing Mumford receives some items from the Meka Leka Magic Store, a reference to Jambi the Genie's magic words, "Meka-leka-hi-meka-hiney-ho."
The Smelly Mystery: If you click on the kite on Page 1, it will say "You know, boys and girls, having your friends stay over really is a lot of fun! I love sleepovers!" and laugh like Pee-Wee.
In his review of Wally Bear and the NO! Gang, the Nerd lists Pee-wee Herman as one of the characters trying to keep kids off drugs in the 80's, referencing an anti-crack PSA that Pee-wee starred in.
In his review of the The Wizard of Oz game for the SNES, after going through a rundown of the game's enemies, the Nerd asks, "Is this Wizard of Oz or Pee-wee's Playhouse?".
In his review of R.O.B. the Robot, the Nerd says that R.O.B. looks like something that Doc Brown or Pee-wee Herman would use.
In part one of his "Wish List" video, some of the items that can be seen the Nerd's collection of Sears and JC Penney's catalogues include Pee-wee's Playhouse toys.
In his review of the Porky'sAtari 2600 game, the Nerd says that the character of Pee-Wee is not to be confused with Pee-Wee Herman.
In his review of Hong Kong '97, Conky can be seen on the cover of the Nerd's fake New York 2017 game.
The Nostalgia Critic: In his review of Beauty and the Beast: The Enchanted Christmas, during the scene where Fife (in his human form) is made the official Maestro of Prince Adam's Castle and plays a song, as an Actor Allusion to Paul Reubens playing both Fife and Pee-Wee, the Critic dubs Fife's song with the Pee-Wee's Playhouse theme song, then asks Fife to at least play a song from the Christmas special.
In the The Adventures of Jimmy Neutron, Boy Genius episode, "Beach Party Mummy", among other things, Sheen says, "Meka-leka-hi-meka-hiney-hiney-ho" when he tries to get a secret passage in the pyramid that Carl is trapped behind to open.
In the Family Guy episode, "Peter Griffin: Husband, Father... Brother?", Peter uses his reparations money from Carter to turn his den into the set from Pee-wee's Playhouse, with Peter dressed as Herman and calling it "Peter's Playhouse".
Peter: Alright, now say it.
Brian:(sigh) Meka-leka-hi-meka-hiney-God, I hate you so much.
A sketch from "Anne Marie's Pride" has Chairy get upset over it being chili day. Pee-wee then arrives with a bowl of chili and eats it as he sits on Chairy, farting afterwards.
A sketch from "More Blood, More Chocolate" has Cowboy Curtis tell Pee-wee that he has cancer, which is revealed to be the secret word.
A sketch from "Zeb and Kevin Erotic Hot Tub Canvas" has the police mistake Pee-Wee and his friends screaming after saying the secret word (which is revealed to be "Over") for a hostage situation.
A sketch from "Fila Ogden in: Maggie's Got a Full Load" involves Chip and Joanna Gaines of Fixer Upper fame renovating Pee-wee's Playhouse for its new owners, Billy and Bethany. Meanwhile, Pee-wee is revealed to have spent the last thirty years looking for his missing bicycle.
A sketch from "May Cause Weebles to Fall Down" involves Pee-Wee and Penny shopping at a grocery store. When Pee-Wee tries to pay for his purchases, the clerk tells him he's two cents short, so Pee-Wee tears Penny's eyes off her face and uses them to pay the clerk.
The Simpsons: In "Marge Gets A Job", a wolf is brought to the Krusty the Clown Show, with the handler warning not to make any loud noises that would spook it. Unfortunately, "loud" is the secret word of the day, and all the screaming and loud noises cause the wolf to run off, where he later attacks Bart.
In the SpongeBob SquarePants episode, "The Algae's Always Greener", Plankton switches lives with Mr. Krabs to find out what it's like. After having to deal with both SpongeBob and Pearl, Plankton says, "Make it stop!", and an alarm goes off. Plankton then asks, "What? Did I say the secret word?".
In "The Looney Beginning", Babs does an impression of Pee-wee Herman as Buster makes a list of what they need to start their own cartoon series.
Pee-wee makes a cameo appearance in "Hollywood Plucky", where he has Hamton, who is working as a valet at Flavio's restaurant, park his bicycle.
In "Fields of Honey", one of Babs' commercials for the Honey theater parodies the series, complete with screaming at the secret word, which is revealed to be "Honey".
The sketch, "Tinkerbunny's Wonderful World of Make-Believe and Learning Fun" (part of "K-ACME TV") spoofs both Pee-wee's Playhouse and Mister Rogers' Neighborhood.
In the short, "Party Crasher Plucky" (part of "A Cat's Eye View"), Plucky imitates Pee-wee Herman in an unsuccessful attempt to get into Shirley MacVaine's party.
In the Direct to Video movie, How I Spent My Vacation, in Fowlmouth and Shirley's sub-plot, Pee-wee Herman is among the customers at the movie theater that Fowlmouth bumps into and has their food spill on him.
