The Angry Video Game Nerd's fight scenes that involve him will have a convenient pile of cardboard boxes spontaneously appear occasionally whenever he knocks someone back, making his opponent fall into the boxes.
Lampshaded when the Nerd and the Critic met. The Angry Video Game Nerd kicks the Nostalgia Critic into a pile of boxes, to which the critic wonders why there are boxes everywhere.
Some gruesome improbable injury happening to George Bush, in a short article ending with the phrase "Bush is resting comfortably at Bethesda Naval Hospital".
A therapist by the name of Eli Wasserbaum will be asked for comment in some articles.
Don Turnbee, a middle aged man featured in articles about his patronage of various fast food establishments.
Any time there is porn mentioned, one of the titles will be an installment of the Butt Fuck Sluts Go Nuts series.
The print version will have a page with a "continuation" of a non-existent article that contains nothing but the phrase "Passerby were amazed by the unusually large amounts of blood" over and over again. Makes for a good space-filler...
Before he died, any article about Strom Thurmond would conclude with "The Senator then died." When he actually died, they ran the headline "Strom Thurmond Finally, Finally Dies"
In their mock history book Our Dumb Century, a few of the running gags included "[Scopes Monkey Trial/Sacco and Vanzetti/Nuremberg/OJ Simpson The Trial of the Century", an editorial cartoon of the Statue of Liberty getting raped/attacked by the menace du jour (The Spanish, Lounge Lizards, capitalist pigs, hippies, Arab terrorists), and an editorial by T. Herman Zweibel declaring "We Must Strike Now While England Is Weak!" at various times in the century.
Their mock atlas Our Dumb World had all the African people named Mtumbe Ngoube.
Clifford Banes, who couldn't be here now as he is currently racing to the airport to find the woman he loves?!
Prominent (American) Congressmen are often portrayed as children learning Very Special Episode style about responsibility, friendship and so on. They're also often attributed quotes in articles on practically any topic; it's just funny to imagine Orrin Hatch declaring, 'Would Al Jourgensen wear a T-shirt depicting smiley aliens telepathing 'Love' to their baggy-pantsed children? Techno should be about hate, not love. Techno is about wearing black and screaming, not standing in one place and swaying peacefully. I say, bring back the days of Skinny Puppy'.
Anytime a church is mentioned, it's nearly always "Holy Christ Almighty [Denomination] Church".
There was a spell when the slideshows featured on the site would always end with the same picture of Alan Alda, which the caption would attempt to loosely tie in to the actual theme.
Before the yusketeers were formed, every time Yusiko met Yumeko or Yukito he would say "we have similar names, we should be friends!"
Ever since starting their Endurance Run, Giant Bomb has made Persona 4 something of a running gag in their website, often making references to the game within their other articles/videos. Within the playthrough itself they have such gags as flanderizing Dojima's already poor parenting, comments about the Funky StudentNPCs and often making voices of Personas they encounter and reject.
All Foundation personnel are reminded that the SCPs are to be treated as powerful and dangerous artifacts at all times. They are not for use in pranks, party games, or to help with your hangover. Explanation Older and sillier articles often have either addenda or notes warning personnel to stop using them for pranks, party games, or as quick hangover remedies. This is being phased out and frowned upon, as a majority of the senior members now find it unfunny, trite, and unprofessional.
"Demoted to Keter Duty/D-Class" Explanation The practice of people committing exceptionally stupid acts being demoted to Keter Duty or D-Class. Nowadays, the former is considered unprofessional; would you want people who broke rules or screwed up a lot being assigned to the most dangerous items? While the latter is just considered plainly stupid and unnecessarily cruel. Unlike funny addenda, this gag serves the purpose of indicating how serious a Noodle Incident can be (like 447 coming into contact with dead bodies), rather than the results of personnel being silly. As such, the practice remains in old SCPs, and is acceptable to use when making references to those old articles.
I Am Not Infected has several, including Paul's sign off ("I'm not infected, at least not the way you think") which refers to his HIV, but not zombie, positive status. A bet between Paul and Charlie concerning getting Charlie to admit he's gay has also come up twice, and will likely come up again.
Whateley Universe examples: Tennyo's constant eating, Jade (who can cast herself into multiple objects) having trouble with personal pronouns, Ayla being picky about food, Jericho's clothing choices, Nate's flatulence problem, Chaka's inability to sit still, ...
raocow's burning hatred of Yoshi, whom he keeps insulting, specifically by calling him a "stupid freakin' horse".
Raocow has a number of these, such as referring to Chargin' Chucks as "Charlie", proclaiming any and all deaths to be purposeful "demos" or "for science", and repeatedly saying "cat planet" on his let's play of cat planet.
Ruby Quest has Tom's MANLY PHYSIQUE and Ruby's GIRLISH FIGURE. And towards the beginning, whenever someone would suggest something dirty (which was often) the response was always some variation on "besides, there might be cameras watching." (There were.)
On youtube one can find a fan-dubbed (in Swedish) version of The Lord of the Rings, titled Sagan om ändringen, meaning "the fairy tale about the change" (the original Swedish title of the first book in the trilogy is Sagan om ringen, meaning "the fairy tale about the ring"). It can be watched with English subtitles, and has a few funny moments here and there, even though the majority is pretty bad. One funny thing though, getting increasingly funny each time it appears, is Frodo's tendancy to sing whenever they are out walking.
Rihanna: You ain't getting under this Chris Brown: Under what? Rihanna: (holds a lamp over 'her' head) Under my umbrella! Chris Brown: That's a lamp. Rihanna: So you think you're some kind of umbrella expert now?!
Wheezy Waiter has a ton here's a video with a bunch of them. later ones include:
Skippy's List has several instances involving an inflatable sheep.
In There Will Be Brawl, whenever someone calls either Mario or Luigi a plumber, they always react with some variation on "We're not plumbers!" Mario always says it with anger, while Luigi says it more with annoyance or resignation. This holds even when Luigi is out of breath from a (small) fight and extended running.
Vegeta trying to give a Badass Boast, often about being a Super Saiyan, only for everyone to be rolling their eyes or be too distracted to pay attention.
Vegeta throwing dog biscuits at foes he decapitates. So far, he's done this to Guldo, Android 19 and Android 15.
Vegeta giving Future Trunks shit whenever any android other than 17 and 18 (whom Trunks believed to be the only ones) appears by saying "Do I hear <number of known androids plus however many extra>?". Lampshaded in Super Android 13 Abridged:
Starting with Episode 17, characters would read the opening disclaimer. Though there are exceptions, said character tends to be killed off, badly injured, or otherwise has something bad happen to them in the episode. Episode 35 lampoons it when Yamcha (having read the last episode's disclaimer with nothing bad happening to him) wonders why he's reading it again.
Just about every fighting group has a guy that's heavily disrespected, either by their peers, by outsiders, or by both. For the Z Warriors it's either Yamcha, or Krillin when Yamcha is not available. For the Saiyans, it was Raditz. For Freeza's lesser minions, it was Appule. For Freeza's personal entourage, it was Dodoria. For the Ginyu Force, it was Guldo. For the Androids, it was Android 19.
Every adventure available at Addventure begins with the protagonist standing before a staircase and having to decide whether to go up or down.
Daffy Duck often hurling himself through the air while yelling "Chuckimation!" (as a reference to a similar "animation" style utilized on KaBlam's Action League Now)
Daffy often complaining about a Golden Book Video not having the space logo at the end of the tape.
Grumpy Dwarf and Daffy freaking out and running away in fear when the aptly-named white screen of death comes up at the end of a tape when it's left running.
Nintendo Direct has several times had someone stare at a piece of fruit (or vegetable) for a few seconds. It started with Satoru Iwata staring at a bunch of bananas in a game showcase after E3 2012. In a Nintendo Direct later that year, Bill Trinen would stare at a tangerine in the same way, and in yet another, a lego version of Iwata was holding a carrot.
Jay periodically has video tapes dropped into his lap. So far, this has happened 4 times:
The original stock of tapes from the Marble Hornets movie.
The supply of tapes and the hard drive he found in his safe after his bout of amnesia.
The additional Marble Hornets tapes that Tim had.
The burnt tapes that Tim found in the hole near the red tower.
In The Gamer's Alliance, there are plenty of running gags. Some examples include variations of the "something warm and floppy" scenes (referring to male genitalia in awkward situations), Nesa bumping into and tormenting the hapless Nightstalker Fred in various amusing ways much to the latter's horror, and Ronove's craving for sand gnome legs and cake during the weirdest scenes.
Starting around episode 32, he's been including at least one tweet from fellow YouTuber Olga Kay in every few episodes of YGS, followed by an exclamation of "OH, OLGA". He even managed to fit it into the Christmas Special, which is a song.
As of recently, using the "poor brian" clip from episode 51 (whenever somebody makes the mistake of spelling "brain" as "brian").
A couple non-YGS examples:
At the end of some videos (before Jack moved to L.A.), Jack's (former) girlfriend Kristen will be there with him, apparently to talk about upcoming videos...but every time, he tells her to shut up as soon as she opens her mouth, leaving her standing there awkwardly.
KassemG and NicePeter's Street Music series has "Superman socks": It originated with the ending of the first video in the series, where they mocked the light blue socks of a man who confronted them for taping him cuddling with a woman in a public park. This was briefly referenced in two other episodes, and the brief melody they used for this bit was eventually expanded into a full three minute song and music video.
Usually when showing just a small part of a game, he'll die at the end of the clip before cutting to something else.
The footage sometimes shows him picking the lowest difficulty setting before starting.
In almost every episode, he'll get attacked by a character from the game he's reviewing.
In quite a few reviews, it's obvious he's using a cheating device as he will get hit, but receive no damage. Played for Laughs, of course.
Third Rate Gamer: And don't ask why I'm not losing any lives when I die.
When words or an image appear on the screen, they are usually followed by a fart sound.
When an image is placed on the screen, he always zooms it in for no reason.
The youtube user Tom Ska has a video titled "Literal Drinks" in which a beverage, referred to as the Recurring Gag, has the side effect of causing a literal recurring gag, and is used as a running gag. Many other tropes take literal form in this video. 
When Shinryuu82 reaches a teleporter Boss Rush in his playthroughs of Mega Man games, he usually cuts the entire segment out with a brief message and sound clip, after which the gameplay resumes with all the bosses defeated. There were a few exceptions to this, such as in his run of Mega Man 42.
In the mail vlogs, people sending Matt origami ninja stars. note In the first mail vlog, a fan sent him an origami ninja star, and nothing else. Matt assumed that it was a folded letter, so he unfolded it, and it turned out that he was wrong. So now, his fans send him origami ninja stars as a joke.
WelshGamer often has a lot of running gags in his corruptions. Such as bringing up the "One-Note Orchestra" when the music in a game plays a single note only, or blurting out "Aliens!" when a scene or screen loops endlessly and lastly, he would say along the lines of "Hey X, gotta go slow, bro." as if tripping when the gameplay and, respectively, the music slows to a crawl. "Don't think about it" when something illogical or confusing happens is also common.
In Ten Words of Wisdom, there are Shiny cowards, who are people who vote a ridiculously large amount of times. One example is an anonymous TWOWgeoisie, who voted over 100,000 times!
"Steve! WHAT BAR is (X)?" began with the Survivor Series 1991 review when Steve V1 likened Randy Savage's ring attire to a Bruiser Bar. Since then, Jay asks this question with an increasingly-camp emphasis in response to colorful ring attire. Steve doesn't just use candy bars; he's compared wrestlers to energy drinks, beer, and sports team colors. It crossed over into The Merch when they unveiled the What Bar? T-shirt.
"Worzel Alert!" (with the Metal Gear Solid "!" alert) comes on in response to Rene Goulet's appearances since the Survivor Series 1990 review, as Hulkamania-era Goulet resembled Worzel Gummidge.
"State of (X)" comes up in response to something terrible, stupid, or silly, e.g. "State of your hair, Greg Valentine."
"Dammit, D'lo" comes up in response to booking the same spot across a card, since D'lo Brown did that for Lockdown when he was a road agent for TNA.
ScrewAttack tends to treat reactions towards the rather controversial Goku Vs. Superman Death Battle as such (such as an advertisement having a Goku Pop Vinyl siding with the side that feel he should've won, a picture depicting a rematch in the Chuck Norris Vs. Segata Sanshiro episode, the topic being brought up in the scrapped Ben Vs. Craig One Minute Melee, and culminated by an actual rematch being released in SGC 2015).
Donkey Kong vs. Knuckles, courtesy of animator xxZackAttackxx: "Oh no."
Random Assault: Mitch being told to shut the fuck up, Tony's ignorance of the letter T, Matt's chronic masturbation.
Decker: The first time any new location is shown, a military timestamp is given. Said timestamp is always the same throughout the entire season.
Free Play seems to have an ongoing war between the confetti cannons, Ryan and the studio's light fittings.
During GetDaved's let's plays, he often awards (or deducts) GetDaved points to the viewers depending on if they understood a reference or if they responded to something in a certain way.
GetDaved: Give yourself ten GetDaved points if your yelling at your screen right now.
Chatting about recent cricket events in the opening. It gets inverted with a listener challenge response to "What mundane hobbies do wrestlers have?" contest: William Regal hosts a cricket podcast but gets constantly sidetracked talking about wrestling.
Bruce Springsteen in the audience challenge segment (Stewart Brooks's favorite musician).
The City Council consistently throwing money into pointless and insane projects.
The creepy music during most "A Word From Our Sponsor" segments cutting out abruptly at the end for Cecil to state the sponsor's name.
Hiram McDaniels' actions consistently being talked about before it's mentioned that he is a five-headed dragon.
Another running gag with Hiram is the fact that he often tries to hide the fact that he is, in fact, a literal five-headed dragon. Cecil will then quote Hiram...and proceed to also quote Hiram's various other heads arguing amongst themselves.
Cecil's inability to return Dana's texts, as every time he tries something horrifically unnatural starts happening to his cell phone and/or his person.
"Hi, this is Joseph Fink... for real this time."
The Who Back When episode of the Big Finish Doctor Who episode "Wirrn Dawn" has long been stalled because of the availability of the audiobook episodes' co-host, jD. As a result, Ponken lists "Wirrn Dawn" as the next audio review for a large number of episodes, and almost every time mentions that he "still hates it."
Revolutions: Referring to John Burgoyne's Sarasota expedition as "Gentleman Johnny's Party Train."
Internet memes are pretty much Running Gags on the Internet as a whole.
PokeSins (a version of CinemaSins for the Pokémon anime) has "Don't be silly [character], X doesn't exist", said whenever a character references something that exists in the real world, but logically shouldn't exist in the world of Pokemon.
Not to mention its creator, Gar1onriva, harping on Ash whenever he calls multiple Pokémon, after a scene in Episode 3 where he declines to do so because...
Ash: The Pokémon League rules say only one at a time. (usually followed by a Minun)