Jackie Chan Adventures has Uncle hitting Jackie in the head with a two-fingered strike each time he does or says something wrong. He also hit other characters such as Captain Black, Tohru, Dark Jackie, Super Moose, and Hsi Wu. In one occasion, he hits himself because he blames himself for the kidnapping of Tohru, and in one episode, he gets hit by Dark Jackie and the two start hitting each other repeatedly.
"One more thing..." Every episode, Jackie insists that Jade stays at home, or with some adult, or at any attraction they were at, only for Jade to find some loophole to his request and just appear on the battle scene; and Jackie is always surprised that she never listens.
And this was lampshaded in a certain episode, with a dialogue that went like:
Jackie:(talking to Jade on the phone) Okay then. But you stay where you are and don't do anything! (turns off phone) Uncle: Jade never doesn't do anything. Jackie: I know, but I feel like I have to say it.
Whenever Archer suspects Lana to have feelings for him, he feels compelled to inform her that she has entered the DAAAYNJA ZOOOONE.
Carol's fetish for getting the SHIT choked out of her.
The absolutely disgusting state of the carpets at ISIS. "Because that's how you get ants."
"Barry, you ass!"
In every adaptation, Sam and Max always fight over answering the phone screaming "I GOT IT! I GOT IT!" Sam always wins. There have only ever been two exceptions to this. In the episode "A Glitch In Time" Max inadvertently changes the timeline, causing Sam to become a mild-mannered monk running a Discount Pet Wash. When the phone rings, Max screams "I GOT IT!", then turns to Sam who just stands there, then sighs and answers the phone.
For the other exception, boogie on down to the entry in the Video Games section.
Other than the obvious ones, such as Kenny dying, there are other, smaller ones such as Cartman's almost unvarying goal to get "ten million dollars". It's never explained why he wants exactly ten million dollars, and the closest they get to it is when another character reveals their own plan to get ten million dollars, they say "that's how scams work."
In "Cartmanland", it is revealed Cartman always wanted one million dollars to buy a theme park. Why he wants the other nine is never shown.
"THEY TOOK OUR JOBS!"
"DEY TOOK ERR JERBS?!"
"DEY TOOKUR JEEOBS!"
DRR TRRKA JRR!!
During the earlier seasons at least, there is at least the outline of one of the aliens from the first episode's heads once per episode. EVERY. SINGLE. EPISODE.
On the DVD release of the first season, Matt and Trey have "Fireside chats" between the episodes, in which they have a dog named "Old Scratch" who changes breed (and even changes into stuffed animals) each time he is seen.
There was also more than one mention of Cartman wanting to give Kyle AIDS. Until he does.
An episode of Garfield and Friends incorporates an intentionally blatant running gag: the episode is framed as a "behind the scenes" documentary where Garfield gives advice on comedy. One of his first pieces of advice is that the secret of humor is to repeat something until it becomes funny. As part of the setup, the lights are often lowered to show a clip. Each time they are to be raised, Garfield calls "Lights!", in response to which several hands appear, offering him lightbulbs. His reaction grows in intensity with each occurrence, starting with "Not funny" and progressing to his final...y being incapacitated by helpless side-splitting laughter when it occurs for the final time.
Timmy's parents often ask him where he got a particular item that he has acquired by wish. Timmy replies, "uuuhh...internet?".
Lampshaded in an episode where this exchange occurs, followed by Dad asking, "and where did you get the Internet?" to which Timmy couldn't respond anything in time, and made his Dad faint because he became suspicious that Timmy was involved in robbery.
When Timmy gets suddenly rich: "Internet... Inheritance... I, uh, inherited the internet!"
When someone brings up Super Toilet, followed by Cosmo freaking out and yelling "So. much. CLOGGING!!".
Although, in one episode where Timmy wishes himself out of existence, we get to see Crocker as he would have been if not driven fairy-mad. He is seen as a highly appreciated philosophy teacher, yet still spasms as he says "EXISTENTIALISM!"
Timmy spasming in Crocker's Day in the Limelight special when he finds out that Crocker had fairies as a kid, immediately followed by him asking his fairies to hit him if he ever did that again. He does, they do.
When Timmy wishes the present was the space-age future that people in the 60s-80s predicted it to become, Crocker becomes a muscular janitor convinced that robots will revolt against humanity and spasms "ROBOTS ARE EVIL!"
Every single episode in this show has its own running gag!
Several very common one often appear:
"Curse you X!"
Mr. Turner's obsession with eggnog.
"Pipe Down!" has a gag where people yell so loudly that their clothes burst right off of them.
Another Butch Hartman series, Tuff Puppy, has some running gags, too. Running gags are apparently Butch's bread and butter for his comedy shows.
D'Nerd from The BOTS Master is a robot that serves as a large databank, and often times would kick into "dictionary mode" to explain the definition of something when the question was meant to receive a more casual response.
ZZ: Hey D'Nerd. What's up? D'Nerd: There are 81 definitions of 'up', which can be used...
On the extremely short-running Clerks: The Animated Series, the second episode is a clipshow (yes, it's absurd; that's the joke), and the running gag is that nearly every time someone says "remember when...", the "memory" clip is a moment from the previous episode — even the "next week on Clerks" clip is this same moment.
One clip that featured four times in said clipshow and remained a Running Gag afterward: Dante and Randal are (apparently) climbing a building using a rope, until a flower pot falls and lands between them. Dante asks, "Why are we walking like this?" and the camera rotates 90 degrees and zooms out.
In addition to the vast number of things that happen Once an Episode, in Phineas and Ferb almost every scene that involves something being built or things being moved around will include the giant creepy-looking baby head from "One Good Scare Oughta Do It!" appearing at some point.
Also, "Aren't you a little young to be [[insert dangerous job here]]?" "Yes, yes we are."
Phineas and Ferb has so many running gags, it might qualify for a gag marathon.
"Ferb, I know what we're gonna do today."
"Hey, where's Perry?" "Oh, there you are, Perry."
Candace and whatever Cassandra Truth she's trying to inform her Mom of this time.
Isabella becoming visibly upset whenever someone uses her Catch Phrase. Anyone but Phineas, that is.
The talking Zebra that calls Candace Kevin shows up a lot, usually when Candace is dreaming or hallucinating. It's even been Lampshaded. She realizes she's dreaming, and says so. Jeremy says that it would explain the talking zebra, but she says that she sees him all the time.
There's a running gag in the series Kim Possible, regarding faithful sidekick Ron Stoppable's disappearing pants. They regularly get slashed open or pulled off of him, exposing his rather colorful collection of boxer shorts. There's even been some Lampshade Hanging on it; in "Showdown at the 'Crooked D'", when confronted with the fact, he claims it's only happened "six or eight times;" in "Exchange," when it happens once again, Ron bemoans his misfortune with a "Oh, man! Even in Japan!"
This itself is almost becoming a running gag; in the episode "Ill Suited", his reaction is "Oh, man! Even as a senior!" This however was lampshaded and solved in Season 4 as Wade made an unbreakable titanium phlebotinum belt for Kim to give Ron.
In "Clean Slate", where Kim gave Ron the belt, he later used the belt to close a steam pipe, thus making his pants fall down again.
Which culminated in a montage of previous falling-pants incidents, as Kim (who was suffering from Easy Amnesia at the time) finally remembered her relationship with Ron, and declared "I love you" to him for the first time. Crowning Moment Of Heartwarming? Yeah.
Without exception, at least once each recurring villain from the Rogues Gallery in Kim Possible has forgotten Ron's name. Senior Sr. and Monkey Fist remember his name a bit better than everyone else, however Dementor and Dr. Drakken have NEVER remembered his name.
Ron himself commented on this in one episode, speaking to Monkey Fist: "You know, you're the only bad guy who ever remembers my name. I respect that."
In the first season, upon seeing an enormous obstacle/opponent that they would have to face, Ron would often exclaim:
Ron: "That would be so cool if it wasn't gonna hurt us!"
Ron being 'micro chipped' by Wade.
The number of almost kisses between Kim and Ron became a gag in season 4. However, if you're a K/R fan, you might see it as a Moment Killer.
Motor Ed's verbal tic. Seriously.
After "Rappin' Drakken," that plan's horrific failure becomes a running gag that spans Season 4 - mostly via Shego's snark or someone only remembering him because of the shampoo. This culminates in him being able to easily put together a Mass Hypnosis plan because "there was plenty of the mind control shampoo left over."
Several episodes, particularly the ones with two shorts that were more humor related instead of one full story, have the running gag of Kim getting stuck with the worst luck or having a much harder time dealing with something while Ron skates through the sitch with good luck and a total lack of interest. This includes Ron being bumped up to first class on a commercial flight - twice - while Kim is stuck in coach (Ron has the decency to try to pretend it wasn't awesome, though he fails), Kim being totally blindsided and humiliated by having the tell the truth all the time while it makes Ron instantly popular, Ron bonding with an overgrown roach monster while Kim is so grossed out she constantly freaks out (after telling Ron not to worry about bugs, no less), both episodes that focus on Felix and the first half of "Sick Day."
Raven: They went into my room. No one should ever go into my room. Cyborg: We're in Raven's room. We should not be in Raven's room. Raven: That's my room! Nobody goes in my room!
Others can be said to be Starfire's culture and its... odities.
Or Cyborg's obsession with food.
Or Beast Boy's obsession with tofu.
Or Starfire's love of foods no-one else would eat. "This tangy yellow beverage is most delicious!" "Uh, Starfire?" "That's mustard." "Is there more?"
The episode "Spellbound" has Raven's obsession with a book she was reading. Each time she read, the scene is visualized for the audience. And every time she's interrupted, the scene would stop/freeze/burn as it would if it were an old-school projector film. It got worse every time Raven is interrupted, as her temper grows shorter.
Beast Boy has very little resistance to hypnosis. And the only thing to get him out of it is to make him laugh. Something that's a running gag in Mad Mod episodes.
In Family Guy: Peter blowing off the front of Cleveland's house while he's in the tub, Joe re-gaining the ability to walk and instantly becoming crippled, Peter's spontaneous battles with a giant chicken, the evil monkey in Chris's closet (Though this one has been resolved).
In an in-episode example ("To Love And Die In Dixie") Peter is attacked by a raccoon at increasingly random times.
The Vaudeville duo "Play me off..." (also resolved), Giggity Giggity, and Stewie talking to Brian about the book he is writing in a high pitched voice are other examples.
Consuela the maid's "No,...no...", and "more Lemon Pledge"
Every time Peter asks if someone has heard, the person says "Heard what?" Peter then proceeds to sing the lyrics to "Surfin' Bird" to an annoying degree. Lampshaded in one episode where Peter loses his memory and turns on a jukebox that plays the song, but Peter unplugs it and says the song is annoying.
A key element of the humor in Harvey Birdman, Attorney at Law is the numerous running gags, from Phil Ken Sebben's "Ha ha... Double Entendre", to Peter Pottamus' "Did you get that thing I sent ya?", to Mentok's mindtaking, to Reducto's paranoia and obsession with small things... It's a long list.
The Transformers wiki often follows up something that makes fans happy with "and there was much rejoicing (yay...)". There are also a multitude of jokes about various incarnations of Ultra Magnus dealing/not dealing with things (based on a line from The Movie). Also, whenever there's a picture of AnimatedStarscream or one of his clones, it's almost inevitably accompanied by a relevant quote about Arnold Rimmer.
Bonecrusher hates that he was forgotten on this list.
Bonecrusher also hates that he was added to this list.
Any image of a bird alternate mode, some sort of flying alternate mode or just tangentially related to flying will be accompanied by the Furmanism "like a vast, predatory bird...".
Furmanisms as a whole.
Movie Optimus Prime wants YOUR FACE.
The infamous "Know that I am Razorclaw" speech from the Universe comic. There are multiple characters named "Razorclaw", and all of them get a reference to it.
Zuko's ship being damaged in Season 1: being buried under an avalanche (ep. 02), being set on fire by Zhao's catapult (07), losing the miniboat over a waterfall (09), being struck by lightning (12), a Shirshu ripping a hole in the deck (15), and finally being blown up in the season finale.
The Cabbage Guy getting his cabbage cart smashed. ("My cabbages!", lapses for the second season before making a surprise return late in the third season when the playwright traveling the world interviewing people to research the Avatar's journey met 'a surprisingly knowledgeable merchant of cabbage'.
In The Legend of Korra Cabbage Corp is mentioned in several episodes before appearing, with a statue of its familiar-looking founder standing by his cart. As the owner is being arrested and his company's assets frozen, he cries out "Not my Cabbage Corp!".
Various characters forgetting that Toph can't see, to the point where Toph once lampshades, "I mean, seriously, what's with you people?! I'm BLIND!" Toph herself isn't above taking advantage of it in order to pick on others, but one time she gets defensive about not being included in an activity that would require sight to do. They also subverted it once where Toph mocks Sokka for asking her to take the wheel of an airship, but he wasn't actually talking to her.
Sokka: Take the wheel! Toph: That's a great idea! Let the blind girl steer the giant airship! Sokka: I was talking to Suki. Toph: That would make a lot more sense...
Taken to extreme when in order to end a rift between Toph and Katara, Sokka writes an apologetic letter supposedly from Toph and sends it to Katara who is not fooled as being blind 'Toph can't write!', Aang still enthusiastically suggests they try again reversing the recipient of the fake letter but Sokka realises 'we may face the same problem'.
Sokka's fake beard in the third season. Then his alias of "Wang Fire" went on to become a Memetic Badass.
Katara's water bending always gets Sokka wet throughout season one followed with
Sokka: KATARA! Katara: Sorry Sokka.
The episode "Comic Book Capers" of Darkwing Duck has a character whose name is Little Running Gag. He threw pies and ran through the scene for no reason. Oh, the name? He was a stereotypical Native American: "Ha! That's my assistant, 'Little Running Gag'." "Oh! I get it. It's a running gag..."
Gosalyn: If you don't come [to Honker's birthday party], I won't clean my room. Drake: You never clean your room. (...) Dark Warrior Duck: I should have recognized you as a bad egg from the start. You never cleaned your room. (...) Darkwing: You're, uh... you're grounded! Gosalyn: Grounded?! What for? Darkwing:(not wanting to tell her he's trying to protect her from Taurus Bulba, now Back from the Dead) Um, for... not picking up your room. Gosalyn: I never pick up my room! You're gonna have to do better than that!
An episode of Tiny Toon Adventures had a similar joke to Darkwing's literal running gag, only with a clown (making it even more literal).
The Weekenders go out for pizza once every weekend... the pizza place is NEVER the same theme twice.
On a few occasions, the pizza restaurant has even changed mid-episode.
A "Treehouse of Horror" episode of The Simpsons had a running gag where Groundskeeper Willie was given the axe. Right in the back. In every story. He acknowledged this in the third story as he was killed.
"OHH, I'm bad at this..."
The Simpsons is full of running gags, including but by no means limited to:
Probably the most famous one, Homer strangling Bart.
If a Simpson shows kindness toward an animal, it WILL be eaten by another animal.
If an elephant shows up in a scene, it's probably going to eat someone.
Animaniacs frequently has Yakko, Wakko, and Dot running by in the other characters' segments, pursued by Ralph the Guard. Pinky and the Brain would also frequently appear in the background in other segments doing the same thing they do every night. Other characters occasionally get into the act as well.
Speaking of Pinky and the Brain, it has its own. In addition to its Once an Episode gags ("The same thing we do every night" and "Are You Pondering What I'm Pondering?"), there's also the matter of Pinky answering Brain's rhetorical questions with a cultural reference that actually fits the question (if not the way Brain intended).
The episode "Survey Ladies" is a one-episode example. The titular survey ladies pop out of everywhere, pestering the Warners. It goes to the point where it's lampshaded by Dot.
Dot:See, it's a running gag thing. I think everyone gets it now.
On Histeria!, Pepper Mills constantly bothers historical celebrities for their autographs, not realizing until after she's gotten it that the person in question is not the pop cultural celebrity she has mistaken them for.
Several episodes have a character suffer a spinal injury and scream "MY SPINE!!"
Beast Wars Transformers has several for the characters; Megatron's "Yessss" and his taking his rubber ducky with him into the regeneration tank, Rattrap and Dinobot's constant exchange of argues, everyone telling Rattrap to shut up whenever he declares that "We're all gonna die!" (which he actually lampshades, once), Waspinator's many, many,manyslaggings, Inferno referring to Megs as "My Queen", etc.
Jim Moralès could tell you all about Code Lyoko's example, but he'd rather not talk about it.
ReBoot actually makes a running joke of the main character, Bob's manycatchphrases ("This is bad...very bad", "Stay frosty!", "That was easy enough"). Having other characters use them, and referring to the fact that if Bob was with them, he'd probably say one of those lines.
Remember that running gag, Al?
In Hey Arnold!, there were two recurring gags throughout the years Brainy sneaking behind Helga and breathing heavily and her punching him, and Eugene always getting involved in some kind of accident usually on his bicycle.
The Venture Bros. includes several, including 24's Nissan Stanza and 21 complaining about not being told about things, such as the fact that the wings on the henchmen's costumes are actually flight-capable.
Monarch and taxi drivers. Every time he has to take a taxi, he either orders that the driver be killed or shoots the driver himself with a tranq dart.
In season 4, every mention of the organization SPHINX was followed up either by a choir saying "Sphinx!" or Shore-Leave saying it himself in his best Camp Gay voice.
Aqua Teen Hunger Force: Any time Shake handles something, which he ends up flinging to the ground, it explodes. Notable examples including from TV remotes, to the Satellite dish he used to cook hot dogs, to three one dollar bills (which took the time to slowly drift to the ground before exploding), and causing a chain reaction once by flinging an object into the television, the object exploding, then the television exploding a few seconds later. It's implied this isn't just a visual gag by charcters silently backing away from the explosion.
Squidbillies: Early Cuyler always robbing the same convenience store, and blowing off the old man's left hand.
Futurama: Roberto robs the same bank three times in a row, in the same episode.
SWAT Kats: Mac can't drive straight no matter what vehicle he's in. Molly loves to remind him of this.
"This is Feral! Bring me chopper backup!"
In Space Ghost Coast to Coast and Cartoon Planet, Space Ghost has what is essentially a reflex to shoot Zorak whenever the latter says something incredibly insulting. This got a skit/episode dedicated to lampshading it in both series. The former had Zorak faking his death after getting shot repeatedly, and the latter had Brak incurring Space Ghost's wrath simply because he "isn't animated to explode" like Zorak is, with the mantis taking all the heat(rays).
Series 9 and 10 of Danger Mouse had Greenback activating a "hit box," which contained a mallet that bopped Stiletto on the head whenever he said something stupid.
Stiletto: Ow! Ow! And Ow!
Young Justice has a few: Kid Flash's habit of picking up souvenirs, Robin's backformations and prefix removal, Superboy's hatred of monkeys, and Artemis nearly drowning has officially been repeated three times, so it counts, too. They're starting to play around the various gags, as well, with Kid Flash complaining about forgetting a souvenir and Robin using one of his created words in a deadly serious context.
On Doug, Mr. Dink always says things are "very expensive". Subverted in an episode where he notes something was "surprisingly cheap".
One can always tell when a Rocky and Bullwinkle adventure is about to come to a close when Boris finds one last thing to say to Natasha as their plans lie in ruins around them:
Boris: SHUT UP YOUR MOUTH!
This running gag even gets a little shout-out during the Oogle Bird adventure, when Boris yells to the bird, "Aw, shut up your beak!"
"Hey Rocky, watch me pull a rabbit out of my hat!"
Superman: The Animated Series: Batman was missing from Gotham and really under Braniac mind control. After Superman as Batman leaves after talking to Gordon, one of the cops standing around remarks "Did he look taller to you?". This is carry-over from the print comic running gag where characters often expect Batman to be taller.
The chief weakness of Planet Sketch was that it tried to make all its jokes into running gags. In the end, there was very little incentive to watch multiple episodes, since they were all exactly the same.
Hot dog stands being knocked over in Ben 10. The joke made a brief reappearance in one of the sequels.
'Victor and Hugo - Bunglers In Crime' - In every episode (with one exception) a small, growling dog would appear out of nowhere, run up Victor's trouser leg and remove his underwear. No explanation is given other than that it is funny - particularly for Hugo.
The daft radio/TV announcements used to open (almost) every episode.
Ned's Newt: Ned's parents entering his room just as he's talking to Newton (the giant shapeshifting newt), upon which Newton quickly transforms into some supposedly innocuous object (such as the Venus of Milo), which Ned's parents remark upon but don't mind too much.
Xiaolin Showdown: Omi's misuse of slang. Even the villains were stunned by the third season.