In Naruto, it is explicitly stated that White Zetsu, being part-plant clone things, do not poop. They're actually rather curious about it, to the point of one asking somebody who until recently did have to poop what it felt like.
Pleasantville makes a point of this — Jennifer enters the bathroom to discover that there are no toilets, because they aren't necessary.
There was some Lampshade Hanging in Galaxy Quest (or in a deleted scene, at any rate) where one of the Thermians mentions to Alan Rickman's character that Earth's "historical documents" (television programs) did not contain any information regarding waste facilities on the ship and "we extrapolated based on your anatomy" - revealing what looked to be the most horrendously painful toilet ever created.
Lampshaded in The Second Foundation, where a girl sneaks aboard a ship and hides there, like she read and saw a lot in popular culture. Then she realizes that the books failed to mention some things, and she cannot remain in her hiding place for long...
Lampshaded in Donaya Haymond's Legends Of Laconia series. In Waking Echoes, the prison cell Ty spends three days in has a toilet, and in Bite Me Matthew asks Dianne if her father goes to the bathroom, saying he's always wondered about those in his condition.
One of the later 1632 books — 1635: The Eastern Front — includes a scene where a radio transmission was delayed because one of General Stearns's staff colonels was "taking care of urgent business."
Lampshaded in the Kevin Brooks novel Lucas - while waiting for the antagonists to walk past, so she can stalk them, Cait realises that she really needs to pee, and she decides to go in some nearby tall grass...only for the antagonists to find her when she's still got her pants down. She muses in her narration that you never see anyone got to the toilet in films, and if you do, it's only because something dramatic is going to happen when they're in the toilet - being attacked by an enemy, for example.
In the Discworld novel Snuff, it's conversed when a little boy whose favourite book so far has been The World Of Poo "was beginning, with encouragement, to read books in which nobody had a bowel movement at all. Which, when you came to think about it, was a mystery all by itself."
The Stephen King short story "Umney's Last Case" features a distraught author trying to muscle out his most famous creation so that he can enter the world of fiction and live without pain. He succeeds, and while the character is getting used to the real world, he wets himself because he's never actually had to use the bathroom before.
Live Action TV
In Hannah Montana, when best friend Lilly Truscott is forced by Miley to go to the toilet, so that Miley can talk to a boy she likes. This is lampshaded when she gets back, after much drama has unfolded with Miley, when Lilly mentions how all the good stuff happens when people go to the toilet.
Whedon was careful to show a toilet on Serenity. The first shot on the show inside a crewman's quarters was Mal zipping up and kicking the toilet back into its resting place.
One U.S. Acres comic had Roy dragging Orson to stop water leaking from a rain storm. When asked how his night was, Orson tells about his dream, he says he went to France and sailed on the ocean, and drank it, thus giving him a fat stomach. Usually when someone drinks too much water, they have to pee, so it would have made more sense if he wet himself in his sleep, but since the comic was for kids, showing Orson wetting himself might have been taboo back in the 80's.
The Trail Of Anguish informs you, "You don't need to use the bathroom right now. It's an adventure game, after all."
EarthBound lampshades the aversion to the trope. They have bathrooms in the game, but they all are occupied or otherwise unusable. In the first bathroom you come to, walking towards the door will result in a cutscene where one guy rushes in ahead of you. Attempting to enter will make him say: "Occupied!"
The title characters of Ren and Stimpy are occasionally seen sitting on the toilet, and from time to time the mother of the boy whose house they were staying at would inform them that "Cartoon characters don't need to use the bathroom!"