With fifteen seasons and over three hundred 40+ minute episodes under its belt, Supernatural had many recurring beats, both narratively and with characters, and many an inside joke that the passionate fandom love. From character quirks to out there jokes that are spread over multiple seasons, the show is rife with running gags and bits.
Some are meant just to be aspects of the character's personalities and the world they live in, but whether it is due to the circumstances surrounding them or the ridiculousness of them, so many running gags work perfectly as bits of levity through the series.
Dean's Protectiveness Of Baby
Dean Winchester is no stranger to close bonds in Supernatural, with Sam, Cas, and even Crowley having unique bonds with him throughout the show. Arguably his most consistent relationship, though, is with Baby.
Dean's protectiveness over his car turns more violent as the years go on. At first, it is merely a warning of Sam to not "douche up" his car, which progresses to the threat of murder should anyone try and steal his beloved Impala.
The Grenade Launcher
The grenade launcher in Supernatural is a fairly deep cut. It appears in the pilot and is a consistent part of the Impala's arsenal but is not used for years, finding itself hung up in Dean's room in the bunker.
As the years go on, a couple of occasions pop up where Dean exclaims his frustration and not needing or being able to use the grenade launcher, even getting excited by Ketch's use of one. Finally, in "Who We Are," Dean got to fulfill his dream of using the launcher.
Dean's Monster Mashups
Despite many of the issues and flaws of Dean Winchester, his deep self-hatred, insecurities, and his neverending restlessness, he is very much capable of having fun with hunting, and something he has done that amuses him massively is come up with monster mashups.
Dean encountered what he called Gorilla-Wolves in Purgatory. Cole's dad was infected by what Dean called a Khan-worm. Other made-up quips from Dean include Wearpire, Octovamp/Vamptopus, Vampirates, Ghoul-Pires, and Manicorns. Of course, his most famous example were creations of Eve, the Jefferson Starships, named so "because they're horrible and hard to kill."
Sam's Height
Throughout the series, a consistent source of comedy and insults is in Sam and Dean's appearance, generally related to either their attractiveness, their flannel, or Sam's height.
Despite only being a couple of inches shorter than Sam, Dean made a handful of jokes throughout the years about Sam's "abnormal" size and was even part of the reason Crowley famously dubbed him Moose, even before the rest of the Rocky and Bullwinkel references.
Cas & Cluelessness
Castiel is a totally different character at the end of Supernatural than the stoic, unemotional angel fans are introduced to in "Lazarus Rising," and his misunderstanding of social situations, humans, and pop culture is a significant part of this.
As soon as he is brought on board by the Winchesters in the fight against, well, everyone, he is constantly not getting basic references, misunderstanding phrases, taking things too literally, and, of course, showing off his lack of skill in pretending to be a federal agent for the first few years of his hunting career. It gets very repetitive over time and arguably outstayed its welcome, holding it back here.
Busty Asian Beauties
There was a handful of running gags from the Kripke-era that died down after season 5 of the show, such as the magic fingers and Dean's love of a specific brand of NSFW material.
"Busty Asian Beauties" popped up time and time again. He went for it both in magazine form and on Sam's laptop and always made sure to pick one up wherever he went, often to Sam's disgust.
Rockstar Aliases
A constant through every season of Supernatural is Sam and Dean taking up different identities through fake IDs, often impersonating federal officers, all in the name of saving people.
Perhaps the highlight of this constant stream of fraud is the fact that Dean makes little effort in making up fake real names; he simply takes up names of famous people he loves, like Hamill and Ford and regular go-to Plant and Page, of course referencing two of Dean's favorite band's members Jimmy Page and Robert Plant.
Sam's Fear Of Clowns
As hunters, Sam and Dean have experienced every type of evil out there, from unimaginable monsters to human psychopaths, to God and the devil themselves. Through all of that, they are rarely scared.
Of course, there is one thing Sam Winchester cannot hack: clowns. His coulrophobia comes up on multiple occasions, both in the form of Dean joking around with his little brother and in Sam finding himself in the unfortunate situation of being around some sort of clown monster such as in "Everybody Loves A Clown," and "Plucky Pennywhistles Magical Menagerie."
Rock, Paper, Scissors
Kicking off in season 2 and popping up time and time again all the way through to season 15, where even the alternate HunterCorps world version of Sam and Dean play a version of it, rock, paper, scissors is a hilarious running gag in the show.
The funniest aspect of the game is the fact that Dean is constantly losing and his reaction to it, with Sam nearly always knowing what he will do. It is both satisfying and hilarious when, in season 11, Dean wins a game and is absolutely over the moon.
Pie
There really is only one answer for what is the best, funniest, and most iconic gag within the Supernatural fandom. It's pie. It is Dean's love of pie, his attachment to pie, his seeking out of the pie, and his rarely actually getting pie.
Kicking off in season 1 and referenced at least once in every season thereafter, Dean is always asking for and about pie, and you cannot help but feel bad for the fact Dean so scarcely gets to actually eat it. One of the most fitting aspects of the unpopular finale is that in a post-God world, Dean wanted to fulfill his dream of going to Pie Fest in Akron.