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.
The Onion's had a Running Gag for the last few months of 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.
"SPC", the common typo of "SCP", is an Alternate Universe version of the Foundation: the Shark Punching Center.
Dr. King and apple seeds. Any time he works with an object that alters or produces something, it always somehow ends up as apple seeds.
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:
Skippys 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.
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 Gamers 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.
The Everything Wrong With series on Cinemasins.com and their Youtube channel has several repeated things across many of their videos that count as sins, including 'Reading', 'Liam Neeson isn't killing anyone in this scene', 'Movie promotes stalking', 'X is a dick to Y' (Y is usually some form of inanimate object) and 'The Prometheus school of running away from things'.
Grif does everything possible to slack off work, and he and Simmons have a current feud over the shotgun seat of the Warthog (despite the fact that Grif usually drives and Simmons takes the mounted turret, leaving Sarge for Shotgun)
Donut is Ambiguously Gay and making anything that can be misconstrued as a double entendre sound like one.
Lopez.0 is regarded as an idiot and speaks in robotic monotone Spanish.
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.
When words or an image appear on the screen, they are usually followed by a fart sound.
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.