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.
In the midst of its Toilet Humour, City Hunter has a magnificent scene that causes Kaori to complain that nobody had ever heard of an hero that goes to poop before the battle, only for Ryo to reply that it's the smart thing to do (and calling her constipated).
A Wizard special focusing on Batman had one questioning if the Batcave has any bathrooms or if Bruce has to run back up to Wayne Manor for a bathroom break.
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(or in a deleted scene, at any rate) where one of the Thermians mentions to Alan Rickman's character that Earth's "historical documents" (television programs) did not contain any information regarding waste facilities on the ship and "we extrapolated based on your anatomy" - revealing what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.
Dave Barry once mused that Batman never goes to the bathroom. "Maybe that's why he's always grimacing."
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 buttoning up and kicking the toilet back into its resting place.
Averted with In The Flesh with an unpleasant overlap with No Dead Body Poops to boot. Zombie Amy cheerfully talks about what happened when she tried to eat, much to the discomfort of Kieran's family. New clothing was required, apparently.
Bridget Hennessey tries to invoke this trope around herself in 8 Simple Rules. She apparently sustains an illusion of never having to use the bathroom.
"Surprisingly, nobody really seems to have to take a dump in fiction. Like, I used to play Elf Forest, which was overly realistic. You could pretty much do anything but relieve bodily wastes. The only game I recall in which you can do that is Simmy Buddies which I think had that toilet meter.
Especially in earlier days and editions of Dungeons & Dragons, when the game's focus was more on world simulation and the detailed logistics of adventuring (counting arrows and torches, keeping track of food and water, deciding who should carry what loot...) were emphasized more, advice on dungeon design would almost inevitably manage to squeeze in a bit about not forgetting that any place inhabited by intelligent living creatures had better include toilets of some sort.
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!"
In Jimmy Neutron vs. Jimmy Negatron, you can at one point make Jimmy go into a bathroom, which triggers a cutscene of him walking out and thanking the player for thinking of it, because he hadn't gone all day.
In Fallout 3 and Fallout: New Vegas your character can drink out of the toilet but cannot use it. Which is even odder in "New Vegas: Hard Core Mode"which makes it much more realistic having your character need to eat and drink and sleep or else eventually die from deprivation. Yet you still do not require toilets.
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!"