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.
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 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.
Histeria! bizarrely re-casts Civil War general William Tecumseh Sherman as Pee-Wee, complete with a Playhouse-esque encampment.