Every time the Elrics are introduced to someone, they greet Al as Fullmetal. Then every other character in the scene points to Ed. Ah, the small one. See above.
Al's armor. Kitties. End of story.
If Edward's gonna transmute something, it'll almost always be in an over-the-top gothic style.
There's a rich couple of innocent bystanders, whose new cars get stolen a lot...
And occasionally a character will be presented with a gift at a time that's awkward and inappropriate, but the person giving the gift doesn't know it and the character receiving will accept it, think for a second and yell about how wrong the whole situation is.
Additionally, everyone associated with the Armstrong family has a Bishie Sparkle. Even the flower lady.
Any time that Colonel Mustang forgets that water is somehow involved, Riza Hawkeye trips him and tells him he's useless. Cue Face Fault and Color Failure on his part.
And his attempts to get her to bathe with him. And his inevitably getting beaten senseless by his wife as a result. And the alien showing up at strange times. And Asuta getting knocked about. And Namiko-sensei's speeches about 'having no boyfriend for 35 years', and the inevitable fall that follows. The show has a lot of running gags.
Sakaki of Azumanga Daioh repeatedly encounters Kamineko throughout the course of the series, who always acts friendly only to bite her hand when she tries to pet it.
There was one episode where various things were said to be "flying" — Yukari's car, Kaorin after Tomo interrupted her photographing Sakaki, the knife in Osaka's hand...
The way Barnaby of Tiger & Bunnyrescues his partner Kotetsu is lampshaded and played for laughs in-series twice out of the three times it makes an appearance. It has even acquired Memetic Mutation status among many members of the fandom.
Kon and Keigo's lechery. Most of the breast jokes revolve around one of them, including an occasion when the shinigami come to the living world and are greeted by Keigo leaping towards Rangiku's breasts. Shortly afterwards, they meet Kon who reacts in the identical fashion to Keigo.
The Shinigami Women's Association constantly holding its meetings on in the sprawling Kuchiki grounds without Byakuya's knowledge or permission and his constant attempts to get rid of them whenever he does find them.
Isshin constantly ambushing and attacking Ichigo at inappropriate times.
How many times do I have to tell you that Ikakku isn't bald?
Yachiru's obsession with his bald head.
A visual example in the anime: The anime goes to extremes to give Ikkaku's shaven head a sparkly twinkly (white tooth smile style) even at the most inappropriate moments.
Hisagi's crush on Rangiku (anime only, the manga barely covers it).
Do not call Hitsugaya a midget (oh, and his voice actor is Edward Elric's voice actor, so the anime loves this one). Or try to give him sweets like he's a child. In fact, don't treat him like a child, full stop.
Rangiku's obsession with shopping (anime only).
The fact Urahara's dimensional gates always always results in its users exiting so high in the sky they wind up having to be rescued by someone who can either help them fly or float gently down to the ground before they tumble to their deaths. Lampshaded in Chapter 487.
Nel: "Aaaah!! The sky! We're up in the sky!"
Ichigo: "Yeah, this is par for the course with Urahara-san's entrances!"
Urahara: "Why, I'm flattered you noticed!"
Not a particularly funny (and actually a little tragic) example, perhaps more Hilarious in Hindsight: every time Leomon (or a Leomon lookalike) shows up in a Digimon series, he's either terribly abused or outright killed in short order.
In Digimon Xros Wars, the Leomon that shows up is a particularly nasty, evil member of The Empire. The same is true for SaberLeomon, one of the twoSacrificial Lions in Digimon Savers. The next humanoid lion to appear in Xros Wars, Apollomon, dies twice within the span of three episodes!
To emphasize, we have Leomon/Saberleomon in Adventure, Leomon in Tamers, Leomon within the first three minutes in X-Evolution, Technically Koichi counts, having Loweemon as one of his forms, and there's IceLeomon too, SaberLeomon AND Bancholeomon in Savers, and in Xros Wars, MadLeomon [Who was a corrupted normal Leomon, who was also shwon revived at one point... and never showed up again, unlike the villagers he was with...], and Apollomon... Twice. And that's just in the main shows and movies, and not counting mangas. 10 dead Lions... possibly 11 if Leomon was killed off-screen in Xros Wars [Which, given how Leomon respond to evil, and the fact that Lillymon, one of the villagers, shows up later... is possible]
The normally serious and Badass Roronoa Zoro of One Piecegets lost anytime he is left alone. Or when he's being led by other people, for that matter. This even extends to the Zombie that is possessed with his shadow. It sort of reached a crescendo post-Time Skip when a ship suddenly appears sliced in two. Guess who's sitting in the crow's nest.
Zoro: "I got on board the wrong ship."
Zoro is also known for sleeping through anything. Even storms at sea, and when the crew is learning important information. He also fell asleep even when he said he wanted to hear Nami's backstory.
Luffy has a tendency to call Mix-and-Match Critters the animal they look the least like. This lead to him calling Bananawani (crocodiles with banana-like growths on their heads) "bananas".
He also refers to anything new as a "Mystery ______". This little quirk was completely absent in the 4Kids dub.
Nami is often adamantly against anything reckless that the crew (aka Luffy) wants to do, but will Heel Face Turn in an instant if there's money involved.
People will mistake Chopper for a different kind of animal (usually a tanuki).
All of Usopp's lies eventually come true.
Sanji's quest to earn himself a bounty. From consistently losing out on getting one to, when he finally does get a bounty, getting a poster featuring a Godawful composite sketch because they couldn't get a good picture (darn tricky lens caps). The topper though, is a man who hated Sanji because his face is near-identical to the godawful composite sketch.
Post-timeskip, his new wanted poster...is a picture of the back of his head.
Robin's tendency to give extremely morbid descriptions
Luffy asking biologically-different creatures if they can poop (notably skeletons and mermaids).
In the anime when the Straw Hats are in Laboon and meet Crocus, they do a series of cuts that end with close-ups of Crocus' eye. It sounds ominous, but ends funny every time. Crocus even lampshades it:
Crocus: "Can't you appreciate a good running gag?"
Luffy has been known to ask any strange person or creature to join his crew, much to the annoyance of his crew (except Robin, who only became a crew member because of his spontaneousness).
In the dub version of the third season of Yu-Gi-Oh! GX, there's something like this involving Martin/Marcel. After being possessed by Yubel, his French accent vanishes, and everyone who talks to him asks "What happened to your accent?" before anything else happens. (This isn't present in the original version, where Martin doesn't speak with an accent.)
And while on the subject, Ryōga from Ranma ½ has getting lost as a major character trait. As Ryōga is an incredibly fit and highly durable martial artist, he is capable of getting very lost, even finding himself in other countries (or even other hemispheres) while trying to travel between two points in Japan. Whenever Ryōga demands to meet Ranma at a specific place and time, he will show up a week late, which is invariably when Ryōga finally finds the place.
Two points in Japan? Ryōga gets lost walking down the street. In one episode of the anime (don't think it happened in the manga) he became hopelessly lost in a park, which had a figure-eight shaped path, and not much else besides trees. Early on, he goes to Cologne's house where Cologne offers to train him. He declines and leaves. Cologne then makes a snack and watches a television show, then goes downstairs to find him still there. He asks her where the front door is. While standing right next to it.
Another Running Gag in said series is main character Ranma Saotome getting splashed by water (usually triggering his Jusenkyō "spring of drowned girl" curse if the water is cold) at the worst possible time. Or just to irritate him.
Miroku's habit of asking EVERY cute girl he meets to bear his child.
And everyone mistaking any demon based on small mammals (Foxes, Otters, etc.) for a Tanuki (dubbed rather well as a Raccoon-dog). Shippo is often at the end of this but other characters get it from time to time.
Jaken saying something that earns a thump from Sesshoumaru.
Yet ANOTHER Rumiko Takahashi series, Urusei Yatsura, is almost nothing but running gags, from Ataru's flirting (inevitably followed by a "Darring no BAKA!(ZAP!)") to Jariten and Ataru's "Frying pan duels" to Shinobu's Desk Tossing.
Another character with notoriously bad sense of direction is Masaki, pilot of Cybuster, from Super Robot Wars OG.
A Running Gag in the Super Robot Wars community is, following mass disappointment of Masaki's failure to appear in SRW Alpha 3, the joke that he tried to get in the game, but got lost.◊
Kusuha Mizuha's "energy drinks", which have laid out not only the greatest badasses Earth can produce, but also augmented humans, cyborgs, aliens, and robots. Ryusei says they do work though, but said drinks are extremely potent
Now Rim may join Kusuha in OGs 2, with her milk concoctions and Chocolate and Jelly filled rice balls. Arado may not have a problem with that though.
Ibis which apparently being a bully victim for well endowed girls, just look at this frickin' scale!
Sailor Moon has many: Ami's obsession with studying, Makoto's always comparing boys to her sempai, Minako's always getting proverbs wrong, Usagi's appetite and unwillingness to study and Rei & Usagi always fighting are only some, and a literalRunning Gag; Usagi being late to school. One that's especially funny is how Chibi-Usa's scepter never works the first time, a joke used a few times during the S season, with even the daimons stopping confused and once in the subsequent season, SuperS.
Prétear the anime: Himeno's older step-sister, Mayune, repeatedly attempts to seduce the Leafe Knights by having them stand outside the bathroom and hold her bathrobe while she takes a shower (usually after meeting in a Crash into Hello-style). This happened to three of them, with the victim escaping each time before Mayune could continue her plan. The fourth time, in the epilogue, she attempted to do this with Mannen, who turned out to be "too young to appreciate her beauty" and just fell asleep.
There's also Yayoi thinking that things happening in real life are like a romance novel, and the butler's pay being cut for things that weren't his fault at all.
Also in the anime, Mayune repeatedly tries to set up traps in order to prank Himeno. For the most part these backfire on her, although Himeno does intentionally walk into one in order to make Mayune happy.
Whenever Van eats in Gun X Sword, he always demands "all the condiments you have". He also tends to yell his reaction to the meal at the top of his voice.
Van's many nicknames.
And Carul Mendoza insisting on being called Carmen99.
As well as Van saying he is a virgin, while whoever he's talking to also being one.
Miu, Strawberry Marshmallow's poster child for ADHD, is frequently the victim of (well-deserved) off-screen violence at the hands of her friends, ranging from a slap upside the head to being chucked out of a spaceship in the "Episode 0" series preview.
The title character of Bludgeoning Angel Dokurochan killing Sakura only to resurrect him a couple seconds later.
Also, in the episode he appears in, Byron's constant and at times unfitting, "I LOVE BASTIODON/STEELIX/FOSSILS/DEFENSE/THIS HOLE!"
Nearly every time Ash's Gible uses Draco Meteor it hits Dawn's Piplup. On at least 2 occasions it's even used to find Piplup.
Iris calling Ash a "kid" when she seems to be the younger of the two.
In the short time period that Meowth tricked the twerps into thinking it had been fired from Team Rocket, and stayed with the twerps, he was nearly caught three times, but always escaped the ball.
Mr. Sukizo, the male judge who keeps saying "remarkable," after reviewing a performance or battle in different Pokemon Contests.
Bianca attempting to glomp something, tripping, and knocking Ash into a pond.
In one episode this happens twice. Poor Bianca looked absolutely mortified.
Wobbuffet and Psyduck popping out of their Pokeballs at inopportune times. Psyduck loves to do it when Misty's trying to call out another Pokemon in battle, and Wobbuffet pops out when Team Rocket's trying to do their evil stuff or say their motto or whatever.
James's Pokemon always show affection in painful ways. His Victrebeel always wanted to eat his head and so did his Carnivine. His Cacnea always tried to hug him.
Ash crossdressing once a region.
Ash's starter fire Pokemon having a rough background before joining up with Ash.
Charmander was left abandoned on a rock for being weak.
Chimchar was abused and overworked to bring out it's Blaze ability.
Tepig was left abandoned and got a rope stuck around it's mouth which caused it to suffer from anorexia for being weak.
Cyndaquil however, was not be subject to a rough background, but instead, ended up joining Ash before being captured by an abusive trainer.
Ash catching the regional bird Pokemon (Pidgeot, Noctowl, Swellow, Staraptor and Unfezant). So far, he's 5 for 5.
Ash's water Pokemon never evolving has become a myth running gag ever since Krabby's evolution all the way back in Kanto.
Regarding the title JoJos; if it's a vehicle, it flies and it contains at least one of them, it will crash. Joseph managed to weaponize this in Part 2.
Polnareff from Part 3 tends to encounter trouble (or something strange) in bathrooms; first, he attempts to use a toilet in India only to find that a live pig's sticking its head out of the commode. Seems that the toilets were placed over a pigsty and the lines weren't dug properly. Later on, when he's attacked by the Stand Justice, he gets trapped in a bathroom; once he's injured by the Stand and placed under its control, he's forced to lick the toilet clean. It's even lampshaded by Joseph, who mentions Polnareff when he's about to use a bathroom in Egypt, where he would have had to let his...dung turn into dust and use sand to clean his hands.
In Mega Man NT Warrior, Lan will call his commander "Mr. Famous"/"Meijin-san" every single time they meet, or he's called. And Meijin always responds with "Just Famous!"/"-san wa iranai."
In Rurouni Kenshin, the other characters made frequent remarks about Kenshin's horrible handwriting.
One could argue that the Pizza Hut Product Placement ascends to the level of a running gag, along with C.C.'s obsession for said pizza and the lengths she'll go to get some.
Lelouch's horrible physical skills, as seen during one Festival Episode where he's outrun even by Milly in a big fancy dress; when, in the penultimate episode, when he makes it up several flights of stairs with relative ease, many fans were shocked.
Yu and his attempts to tape the Midnight Channel programs.
Aika making deliveries/working in increasing unlikely places. Not only does she work at Aiya, make a delivery in the middle of a chase scene, and bring food to the protagonists on top of a mountain in the middle of the school camping trip, but she also has a job at a noodle shop at Tatsumi Port Island and at the Amagi Inn. They try to explain away the job at Tatsumi Port Island, but by the Amagi Inn episode, the writers stopped caring.
Scenery Censor: In addition to Censor Steam, episode 20 uses this to hide the girls' lady bits from the audience. There are many, many conveniently positioned arms. At one point, a washtub held at a funny angle is used to hide Naoto's entire upper half.
Eyeshield 21: Mamori not being able to draw, Monta being mistaken for/compared to a monkey, Ishimaru being forgotten about or not noticed i.e. Demoted to Extra, the Shinryuuji Nagas (who attend an all-boys school) being distracted by girls, Shin's technological impairment, Otawara forgetting to wear clothes, the Ha Ha Brothers having to remind people that they are not actually bothers and/or are separate people...there are a few.
Haruhi's obliviousness to others' attraction to her (usually culminating in her asking "Do you mean [obscure interpretation of professed attraction]?") is repeatedly played for laughs in Ouran High School Host Club, finally lampshaded when one of the boys asks her to go out with him:
Haruhi: "Do you mean—" Hikaru: "No, I do not mean "Will you go somewhere with me?" I'm asking you on a date."
His habit of going through Color Failure when anything traumatic happens, usually relating to Haruhi. Bonus points for when characters break the fourth wall and comment "Oh, Tamaki has gone all white again" "Look at him crumble into powder and disappear."
Hikaru and Kaoru discard a banana peel and someone slips on it, pretty much Once an Episodeat least!
Dinosaur King: Ursula being called an old lady (which always hits her Berserk Button), and her noticing it, no matter how far away she is, and getting mightily offended. In one episode, this became a plot point-Ursula's uncanny hearing allowed her to find the D-Team after they referred to her as 'old lady' one too many times.
Cagalli Yula Atha of Gundam SEED is repeatedly mistaken for a boy, first by Kira and then by Athrun. Her hatred of dresses, despite being a princess and her said displeasure at mistaken gender, also reoccur throughout the series (both in Seed and Destiny).
Patrick Colasour of Gundam 00 cannot die. No matter how spectacularly he fails in battle, he always lives through it. The other characters notice and mockingly nickname him "The Immortal Colasour".
He gains a second Running Gag in The Movie, where he can never remember to call Kati Mannequin by her new rank: Brigadier General. He always refers to her as "Colonel". Did we mention they are also married by this point?
Gundam 00 subverts the "It's a GUNDAM!!!" meme. Even though it's said every other battle, everyone from mooks to major characters, most of the people who say it survive, or, in the case of mooks, aren't necessarily among the dead.
In Soul Eater, anyone who's ever had the misfortune of encountering Excalibur will inevitably get the same, identical, pained expression on their face when he's mentioned in their presence, at the same time.
Even The Table Of Contents grows a face simply to show his frustration/pain at Excalibur's existence.
Black*Star failing to sneak up on anyone because of his Voice.
Death the Kid whenever he encounters something unsymmetrical.
Bonus points when he does said unsymmetrical thing he gets on his slumps on his knees and starts pounding the ground.
Death the Kid: "I'm a hideous pig. <Insert the unsymmetrical thing what he did> I'm a worthless piece of garbage. I deserve to die."
In many a romantic-comedy anime such as Love Hina, where a Tsundere female protagonist's daily beating the crap out of the male protagonist is used as a primary source of laughs, expect her assaults become increasingly more violent to keep the joke going, despite the fact that their growing relationship should cause it to be the exact opposite.
In Moon Phase, pans, metal objects, and such, will fall on characters' (who take no notice) heads with a loud CLANG! many times per episode, happening more and more frequently over the course of the series. Whether the scene is comedic or dramatic, with no bias.
In s-CRY-ed, Kimishima's' ride would constantly get smashed (or destroyed in some odd way), causing to cry out (or a variant of), "NOT THE CAR!"
In Keroro Gunsou if something lands at the Hinata household, you can be sure it will land on Giroro's tent. Bonus points if he's inside it when it happens.
The Mahorafest Arc had Takane D. Goodman, who ended up getting stripped naked every time she showed up. Using magically summoned clothes is bad idea when 1) they disappear when you faint, and 2) the lead heroine uses Anti-Magic. Even the other characters start calling her a stripper, despite the fact that in the Negiverse Clothing Damage is a regular occurrence.
Clothing Damage in general has gotten to this point. Asuna ( well, actually Shiori, but she's copied Asuna's personality) actually asks Negi if he's capable of getting anything done without blasting people's clothes off.
There's also the gag where Koyomi attempts to use her artifact repeatedly, but is always foiled by Jack Rakan flipping her skirt up after stealing her panties. It's happened on at least three separate occasions.
The series of visual running gags included in each episode after their debut, consisting of: The dog with a stick up its ass, the stork, Kaere's random panty shots.
There's also Apachai constantly answering the phone with some variant of "Hello. We have your child."
Sakaki acting like he doesn't care about Kenichi when he worries about the kid more than any other master. And getting called on it. It's gotten so bad that SHIGURE has started making fun of him for this.
Fushigi Yuugi's list of running gags consists of the following:
Tamahome's Money Fetish, even after it's revealed that he uses his money to support his poor family. And the gag still goes on after his family is brutally murdered by Suboshi.
Hotohori praising himself and his totalgorgeousness, as well as his getting mistaken for a girl.
Chichiri's frequent appearance in Super-Deformed form counts as well, as he does it in extremely inappropriate situations and it is lampshaded by Tasuki later on.
Tasuki burning Tamahome with the tessen and claiming each time that it's an accident, as well as getting clobbered by either Tamahome or Nuriko.
Tama-neko's charades and being mistaken for Chichiri.
Subverted: The times it's actually used in-stry can be counted with the fingers of your hands. Fanongreatly exaggerates how common is it.
People forgetting who Canada is.
Italy's first instinct in battle — making a white flag and instantly surrendering.
Every single character seems to have one, to some extent: America and his hero complex, Belarus's 'married married married', Prussia and his 'awesomeness', England's cooking and his fairies, Russia and his Slasher Smile (and the pipe! The pipe!) and so on and so forth?
Whenever Himaruya draws a character that no one recognizes, it's pretty certain that someone will comment with, "It's Mexi-/shot"
The same metal bucket keeps showing up (Randomly falling from the sky onto Italy's head, Switzerland pulling it out of nowhere and putting it over his head)
The announcer-lady in the American dubbed has a habit of insulting its viewers, well, more so American-anime viewers at any rate.
Chrono Crusade: Rosette violently responding to something Chrono said, normally meant to be a barb by him, but not always. The manga also has Satella flirting with Chrono because she "likes younger boys" and Joshua hating carrots.
In Episode 11 of Princess Tutu, Ahiru forgets that she's naked when she transforms from her duck form to her girl form and transforms in front of Fakir, who responds by blushing and holding out her clothing, then throwing them at her when she forgets she's naked again. By the time the second season rolled around, there was a running gag of her transforming around Fakir (often with Uzura's help) and him reacting in increasingly over-the-top ways. There's also Uzura's obsession with people's tails and "lovey-dovey", Professor Cat threatening Ahiru with marriage and Autor yelling at people to be quiet in the library. Fandom has also decided that Mytho not liking to wear pants is a running gag, although it's hard to tell if this was meant to be a gag or not.
Cromartie High School: Nobody except the main characters realizing that Mechazawa is a robot (including Mechazawa himself), Hokudo's Lackey being interrupted before he can tell someone his real name.
At least in the anime, 2 out of 3 field trips are cancelled or go completely wrong. The one that goes 'well' (i.e., where the class actually arrives at its intended destination) has Takanouchi pass out. So in essence, Takanouchi missing out on all the field trips is the real Running Gag.
Anytime Bass High kidnaps somebody, that somebody will be Maeda, every time.
Gintama: Alright, stay calm. We just need to find a time machine...
Expect many characters voiced by Kikuko Inoue to declare that she's 17 years old, be they from anime or video game. Because she did so in real life and formed a club about it!
Guy fails to recognize Kisame every time they clash, which Kisame takes great umbrage in. In chapter 505, Guy managed to mistake Kisame for his own dark side due to some bizarre timing, and laid him out before processing the warning others were shouting that Kisame wasn't. Every time they meet just gets funnier and funnier. In a complete reversal of this gag, after Kisame bites off his own tongue and makes his summoned sharks eat him alive to protect Akatsuki Guy is so impressed that he vows to remember him forever.
There's also Shino taking issue with frequently being ignored or left out, culminating in this exchange:
Shino: "We must avoid drawing attention to ourselves." Ino: "You'll be fine, Shino."
Kakashi being purposely late for mostly everything.
Naruto charging out enthusiatically and then stopping abruptly to ask, "Where is this place anyway?"
Sakura punching Naruto.
Naruto also has a knack of being forced to swallow extremely unpleasant things, including huge insects, a frog whose midsection is a scroll, and even a crow.
In Great Teacher Onizuka, Hiroshi Uchiyamada's Cresta constantly gets damaged badly due to accidents, much to Uchiyamada's dismay.
A Certain Magical Index has plenty of these, usually involving Touma's immense misfortune. There's also Misaka's tendency to chase down and try to electrocute Touma in A Certain Scientific Railgun anytime she sees him (several times she chases him for a whole day and well into the night).
Almost every Index arc ends with Touma in the hospital. If he gets through an arc without getting injured, he'll still go to the hospital to say, "Hello" to everybody.
A frequent, rather hilarious visual joke in Baka To Test To Shoukanjuu involves an Art Shift, Yuuji placing his hand on Akihisa's shoulder, saying something in a sagacious manner, and Akihisa looking back in awe, often while saying "Yuuji...".
Trigun has the black cat Kuroneko-sama appearing in every episode without fail (even in the Flashback episode; look in the statis capsules), and usually in some funny manner.
In Gakuen Babysitters, Kotarou will often either call the Chairman "Fluffy" due to her large and extremely curly hair or point out something with as fluffy texture or appearance in reference to her.
In 3-gatsu no Lion, Akari's cats, who have been spoiled somewhat due to her care, will often beg or react wildly to the sight, and sometimes even mention, of food and/or dinner.
The Yellow Flag bar in Black Lagoon has been constantly trashed and flat out blown up on a regular basis over the course of the series. It's owner, Bao, actually has kept count of how many times this has occurred (15 times trashed, 6 times completely annihilated, to be exact). Despite this, Bao has rebuilt every single time.
In K the usually serious Kuroh starts blushing like a schoolgirl and uses his cassette to play the recorded voice of his former master, Ichigen Miwa, whenever his name comes up. It's always followed by Yashiro saying "Creepy!"
Yuru Yuri has a ton, like Akari's lack of presence and Sakurako's jealousy of Himawari's chest.
