Levi from Attack on Titan is prone to this kind of snark. When Erwin is late for a meeting, Levi suggests it's because he's stuck in the bathroom due to constipation.
Better because it's Levi, ofallpeople, and he phrases it:
Levi: Maybe he's taking a shit and the shit won't come out.
A Running Gag in Black Clover is that people tend to barge in on the Black Bulls' bathroom while the squad's captain, Yami, is trying to take a dump. The typical response is Yami threatening to kill them (and usually demanding more toilet paper), causing the offender to run in terror.
Makes up a good deal of the humor in Bobobo-bo Bo-bobo. In particular, it's the specialty of Gasser and anyone talking about Softon (whose head is shaped like... ahem, chocolate soft-serve custard... yeah).
Makoto-chan, ancestor of Crayon Shin-chan, is obsessed with poop and weenie jokes. Heck, the movie has one skit that consists of Makoto and his sister performing a play for their parents using their genitals.
To quote his Funimation VA, most of Shin Nohara's dialogue pretty much consists of "Farty poop fartfart". The original isn't any better; Shinosuke's problem with constipation keeps being discussed and his underwear is noted to have skid marks.
Digimon Adventure seemed to have a thing for Digimon relieving themselves everywhere at the least appropriate times, best exemplified by the Numemon species which attacks solely through flinging its shit. Thankfully, after one final instance of a urinating angry Tortomon being a Monster of the Week in Digimon Adventure 02, the rest of the franchise has pretty much discarded this brand of humour (and whenever a Numemon appears it's never clarified that they're flinging faeces).
Not to forget Sukamon who basically is a giant talking turd. There was a toilet-humour filled omake about it in the V-Tamer manga.
Akira Toriyama is a master of this, with it forming a lot of the basis for Dr. Slump, and to a lesser degree the early years of Dragon Ball. It's worth mentioning that Dr. Slump even goes as far as not only turning poop into a side character, but actually even giving it its own episode.
Gintama has no shortage of this, with vomit being the most common form of it. The fact that they use Pixellation on it only serves to make it more amusing.
Hajime no Ippo loves doing this. Especially when Takamura is involved.
One of Kagura's first moments in the OVA has her purposefully make a scene by having herself vomit on a public street, after which she proceeds to brag about being the first Shounen Jump heroine to have pulled off such a stunt.
The Bentendo Owee arc has Shinpachi and Yamazaki compete against each other in a game of Nobunaga's Regurgitation, which is essentially Tetris, but using pixellated vomit for the blocks.
InuYasha has scores of this here and there. Most noticeably, the episodes "The Snow from Seven Years Past" where we have yellow snow and Miroku gettingpeed on in the face... Then again, it's not the first time Miroku has been peed on or mistaken for a toilet...
Episode 2, which deals first with a ropes of snot covering the cast, then with the dojikko nurse spilling urine samples everywhere; on the clothes, in the hair, in open wounds, in the eyes, in coffee...
The potty humor doesn't really return until Zoryochu episode 6, which doesn't go as far, first having the triplets experience a Potty Emergency after eating rotten oranges, then with Mitsuba making snowballs out of snow that Chiba had peed on.
Naruto had a few examples early on, namely in the second episode of the anime where Naruto drinks badly spoiled milk, then his shadow clones all get diarrhea at once, fighting to get to the bathroom.
In the Chunin Exam, Naruto won his match against Kiba strictly through a fortuitously timed fart that momentarily stunned Kiba when he had enhanced his sense of smell several hundred times. It became a Running Gag; every time Naruto farted, Kiba was always in the vicinity.
Also Naruto had a habit for stepping in dog poop, not to mention Akamaru peed on his face once.
In episode 482 of Shippuden, a young Kankuro tells his brother Gaara to make sand-structures out of various foods. He then asks him to make a giant poop out of sand. Temari facepalms at Kankuro's immaturity.
While most of the humor in One Piece doesn't rely on this, the series has its moments. For example, three of the characters (Franky and Hotori/Kotori) use farts as weapons. One of Brook's quirks is that he pretends to be a gentleman, but always burps and farts at meals. And then there was a scene in Skypiea where Luffy, Nami and some other characters were trapped in the belly of a giant snake. Luffy immediately suggested that they should find their way out through its asshole.
Kinemon is able to talk through his butt via farting.
In the first episode of Orphen, the main character, Orphen, gets crapped on by a bird.
Sailor Moon deals with this in a side-story in the Dream arc, related to Rei and Minako's exams for high school. A gag revolves around the 5 girls having a slumber party and asking each other weird kinds of questions, such as Minako asking Rei if she's ever farted. When Rei got mad at Minako at the end of the story, she professes that she has never farted but that Minako does all the time, and thus they're truly not compatible.
The first anime has its own key examples, with Usagi mainly being the butt of the jokes. One episode of R winds up having her fart in the presence of the other girls due to her eating a sweet potato, and a gag in Super S revolves around her farting in an artist's presence. The S drama CD also has a skit where Usagi goes to visit Haruka and Michiru, and Usagi's unladylike farting is contrasted against the elegant Michiru, who claims to never fart or poop— to the point where she and Haruka apparently don't have toilets.
A punchline in another episode of the R anime revolves around Usagi discovering that Chibiusa climbed into her bed and wound up wetting it, which causes her to be spotted cleaning out her sheets later on, with her brother mocking her and believing she wet the bed. Even Luna initially believed that Usagi wet the bed at the start of the episode, until they found Chibiusa hiding under the blanket.
7 Seeds is overall pretty realistic and vague about things, but two instances stand out in giving us flat out Toilet Humor.
The first is during the Dry Season and Played for Laughs, Semimaru goes off a bit to go pee. Urine splashing over what looks like half-buried dead dinosaurs causes them to awaken. It makes them realize that these dinosaurs and monsters aren't dead, but merely hibernating through the dry season and, if they do not leave before the rainy season comes back, they will all be rehydrated and attack them.
During the weird chapter that is Applause, Child!Hana eats something that doesn't become her well and she runs off to poop into the ocean. She poops some more, amused because she saw insects eating her feces in the water.
In an early episode of the Monster Rancher anime series, Hare and Tiger are fighting in a tournament. In the original Japanese version (as well as many foreign versions), Hare wins the fight by tricking Tiger into letting his guard down and farting on him and the smell is so foul it knocks Tiger out. This scene is cut from the American dub and instead, Hare wins by punching Tiger out.
Sgt. Frog has lots of fart jokes. There's also a manga chapter, "The Shocking Survivalist Sergeant", where Keroro holes up in the Hinata family bathroom after an argument with Natsumi, and ends up taking a bath in the toilet.
One of Shonen Jump's most popular gag series of the 70's was the appropriatelly titled Professor Toilet.
There isn't a single kind of human waste that didn't make it into Super Radical Gag Family.
This is somewhat of a running gag seeing how she not only does this again in the 3rd ova as well, but also in the video game depending on the scenario.
Episode 7 of Tenchi Muyo! shows that Ryoko has No Sense of Personal Space. By phasing through the wall of the bathroom while Tenchi's using it and being quite proud of "Lil' Tenchi". The next scene shows Ryoko pawing at the door and Tenchi telling her to stay out.
Tokyo Magnitude 8.0 has a literal toilet related joke, which is unusual since the series is a solemn but still mostly idealistic take on the events after an earthquake. Yuuki, who is around eight year old, is amazed by a disposable paper toilet and pretends to poop in it. His sister is too embarrassed to use the toilet and spends a good chunk of the episode avoiding a Potty Failure and trying to find a "normal" toilet but ends up using the disposable one.
In Episode 7 of Sword Art Online, Kirito and Asuna encounter a crystal-eating dragon, and upon finding a "crystal" in the dragon's nest...they find out that its dung is in the form of crystals too.
One episode has Nate pooping in the school bathroom. A yokai makes his crush Katie repeatedly state this, once in front of his class and once in front of her friends. He is understandably horribly embarrassed.
Cheeksqueak's debut episode is nothing but toilet humor. Cheeksqueak is a yokai whose face looks like a butt and who makes people fart in inappropriate and embarrassing situations. Even Katie isn't safe from the yokai, despite Nate thinking girls don't fart.
There is a yokai that makes you have to pee. He caused a lot of trouble for Nate and his friends.
Yondemasu Yo Azazelsan is also a prime example, what with feces being an essential part of fly demon Beelzebub's diet.