Running Gag/Fan Works

Secret Services do not exist in Aeon Natum Engel.
In Touhou Project fanfiction, Marisa always seems to be stealing Patchouli's books.
- We probably shouldn't get into Touhou running gags from a fandom perspective or we'll be here all day. There's few characters that don't have three or four running gags to their name.
A Very Potter Musical has several:
- Hermione losing House points (for reasons that get more and more blatantly unfair each time), followed by a sarcastic "Thanks, Hermione" from Ron and Harry.
- Gryffindor losing points - again, each time is increasingly ridiculous.

Severus Snape: (to Draco Malfoy) Coward! Ten points from Gryffindor!

- Ron's snacks.
- Draco rolling around on the floor for emphasis.
- Some might find Cedric's puns about Hufflepuffs being great finders to be a running gag.
- In the sequel: diapers, Redvines, who James Potter's best friend was...
In the Mass Effect self-insert Mass Vexations, Author Avatar Art introduces The Game to Urdnot Wrex. There isn't a single conversation that they have afterwards where Wrex doesn't try to make Art lose the game.
- And, as of MV2, Wrex has taught ALL OF TUCHANKA about the game. ALL OF IT. Art loudly makes Wrex lose the game and the entire room of Krogans goes "Oh, dammit!"
In the Mass Effect fics Inglorious Boshtets and Project Gethinator, neither Tali nor Shepard can seem to go through a single mission without something going kaboom.
In Kyon: Big Damn Hero, Kyon reminds himself he has a very special hell waiting just for him after kissing Haruhi, the older Mikuru and Yuki.
- Also, the very first line readable from a letter from the future is an commentary in context of the conversation.

Haruhi: Can I go (time travelling) with you?
Kyon: (reading the letter) "No, she can't."

- Kyon's habit of sending greetings to himself when Time Travelling.
- Kyon's remarks about how his past and future selves are annoying, then laughing at his past self for doing something stupid.
Total Drama Comeback Series, the most notable Total Drama Island Fanfic, has Beth asking a question that reveals a certain detail about the challenge Chris would have forgotten.

Beth: Chris, what about * insert detail about challenge*
Chris: Why thank you Beth, here have a cookie.

- it was a sad day when Chris ran out of cookies
In the classic Mad parody of G.I. Joe, women would fling themselves onto the hero's lap and say, "Hey, Joe! You got chewing gum?" This gag resurfaced in at least one later Mad feature.
Dragon Ball Abridged has the Krillin Owned Count, which is fairly self-explanatory. Prior to Episode 25, he has been owned 14 times. Frieza then bumps him up eleven more for a total of 25 (and two 1ups to boot).
- For the Planet Namek arc, virtually everything referenced that should be alien simply has "Space" tacked on in front of an Earth reference.
- "Kaio-wha-"[blow to the face]
The multi fandom crossover series, Chance Encounter has a couple of these.
- One is Balian a) insisting 'it feels worse than it is' or variants thereof b) Balian's numerous attempts to escape whichever infirmary he is in this time, being something of the Butt Monkey (he gets beaten up repeatedly, usually after doing something stupidly heroic and getting outnumbered).
- 'Nanny Balian' and 'Nurse Legolas' (or according to Jack Sparrow, Nurse Legless, somewhat ironic as he spends most of his time drunk). This last one also doubles as a Berserk Button for both of them. Also, 'Truly, it is not a coincidence' or some variation on the theme, however this can be seen as arc words, referring to divine meddling. The author is rather fond of the phrase, using it in a separate but similar fic.
Progress has poor Princess Luna getting bashed and battered by baseballs. That, and her attachment to her abacus, which has become a bit of a running gag in itself because it gets shout outs in other fan-fics.
There are two in With Strings Attached:
- When the four first meet the exiled skahs wizard Lyndess, she immediately asks them, “What are you selling, olyrr-sars [outworlders]?” When they are sent to Ta'akan, every single person they meet thereafter asks them the same question, until word finally spreads that they have nothing to sell. (At one point a very annoyed John comments that if they get asked that stupid question one more time, he's going to pull his trousers down and say “Yeah.”) Much later, when the Hunter is brought to Ta'akan, he gets swamped with people asking him that.
- There's a literal Running Gag that starts in the New Zork chapter. Ringo finds himself yanked, dragged, and carried around by practically everyone he meets. This includes a pair of disembodied arms that throw him off a roof, Beagle Brian Epstein, some cops, Flyboy from the “Hitler Youth,” and John. He gets picked up and carried in someone's arms several more times during the book (including twice during the climactic assault on the warehouse), and at one point the Hunter offers to carry him.
In Turnabout Storm, everypony seems to think that Phoenix Wright's hair it's some sort of beast or critter every time they first see him. It's not like you can blame them.
Mars Attacks: Simpsons had a random character call a random location or person for a prank in each chapter.
Paperwork in the Worm Alternate Universe Fic Mauling Snarks -- it seems like someone has to fill out paperwork for something every single day, and the variety and purposes of the forms to be filled out sometimes reaches pinnacles of absurdity -- there's a form that has to be completed in order to play a prank on someone in the PRT building, for instance. Played with In-Universe with the requirements for submitting oneself to a tinker fugue, which are ridiculously (and intentionally) over-the-top and complex, combining excessive paperwork with what for all purposes is a scavenger hunt.
- Another in-universe running gag -- referred to as such by the participants -- exists, in which the Wards are subject to a conspiracy of silence about the courses and resources available to them, with the intention of teaching them to ask questions rather than just accept things as they seem to be. Those participating in the conspiracy gladly answer all questions, but do not volunteer any information, not even to suggest that the Wards should be asking questions.