Making any variation of a "Thinking with Portals" joke throughout both Portal Let's Try That Agains.
Oftentimes, when Ricky exclaims "Oh shit!", Josh will follow it up with "It's the SA-X!" or "NOVA blows up!" Both being references to things Ricky has said before.
Some running gags actually come in the post editing phase of the videos. Recently, whenever Kyle excitedly says "Ooh! Ooh! Ooh! Ooh!", a picture of a smiling monkey appears on the screen.
"What does that have to do with Fossil Fighters?"
"This is getting Cofagrigus."
Josh is trying to get "nipped that in the bud" to catch on.
Whenever someone says something random or just weird, someone else is bound to say, "That's an intro quote." If the person continues to say random weird things multiple times, someone else will usually say something like, "You're just fishing for intro quotes!"
Whenever Matt uses his "rap team" in Pokemon Showdown, he'll usually recite a part of a rap by whatever Pokemon he's using.
(sends out Drake the Scrafty)
Matt: Last name ever, first name greatest...
Some running gags even come from the fan community. For example, whenever anybody comes back from being away, it's common for somebody else to great them with "Warner Bros." This comes from Don taking the abbreviation for "Welcome Back," WB, in a different direction and fan (maryann2573) bringing it up in pretty much every stream from that point on.
Another fan created running joke is "Vote Jess." "Vote Jess" references a joke made about Jess running for senator after Adamant Ditto ends.
The fact that the group relies so heavily on running gags has become a running gag in and of itself. Often times, when a long-running gag is mentioned, someone will make fun of it and claim they only have "six jokes."
"He got two!"
Usually when Jess laughs, #Jess Laugh pops up on the screen.