A popular The Legend of ZeldaHigh School A.U. called "Ordinary Story" has Zelda as a boarder in Link's adopted family's house in Florida. The story eventually proceeds to ditch its AU status when Zelda finds the Ocarina of Time, she and Link start to unwillingly inherit the Triforce, and a man named Ganondorf shows up to take over Zelda's father's company. However, there are a few scenes in the story that make reference to Link and his friends playing the Nintendo GameCube, a console he himself appears on in this universe.
In the Jackie Chan Adventures and W.I.T.C.H. crossover fic KageJade is nonexistent on the Earth the Guardians are from. She is replaced by Stacie Chan, who, like Jackie's real life niece who voiced Jade for the cartoon, wants to follow her uncle's footsteps as an actor.
In Parable of a Boy Named Gregory, a South Park fanfic of epic length that pairs Gregory and Pip, Gregory is interviewed on Larry King Live after having escaped from the military base of North Korean invaders on American soil (don't ask); when Larry King asks him whether or not Gregory's hometown of South Park, Colorado has anything to do with the TV show "South Park," Gregory is extremely confused, never having heard of the show.
Often, in 'Human in Equestria' (or vice-versa) fics, if the main character is a brony, then there is a subplot as to how both the characters and the show exist at the same time.
This is often played frustratingly straight in bad fanfiction. There are countless mediocre video game fics where the characters would play games from their own series; the author usually wouldn't even bother to Hand Wave why Sonic's son was playing Sonic Adventure 2: Battle. We're apparently just left to assume there's No Fourth Wall, but it's still irritating.
In a very good Kingdom Hearts fan-fic, The Annals of Darkness, there are many references back to the Kingdom Hearts videogames, Hand Waved by the explanation that Sora and co's adventures have become so well known that videogames have been created about them. Played with by having Sora give Max Goof advice on how to beat certain boss battles.
In one NCIS fanfic, Hocus Pocus is discussed. However, Sean Murray doesn't exist and McGee is teased by the team (mainly Tony, of course), because they have found out that he starred in a kind of stupid movie about witches when he was younger.
Averted and acknowledged in the infamous Marissa Picard series. Star Trek (the media franchise) really did exist in the Star Trek universe, but was eventually classified and buried once "reality" started following "fiction."
A hidden bonus in one of the panels of the fan comicHalo: A Fistful of Arrows reveals Bungie is still around in the 26th century. One wonders what their "killer app" from the Xbox was in this universe.
In A Time to Kill, mention is made that James Bond the secret agent co-exists in the same universe with the Bond film series. Some Applied Phlebotinum explains away how Bond is able to get away with it, but no mention is made why all of Bond's separate incarnations tend to look like the same actors in the film series.
In the Discworld sci-fi/fantasy fic Slipping Between Worlds, Philip Holtack, a resident of Earth who inadvertently arrives in Ankh-Morpork, has this sort of conversation with HEX, the University's thinking engine (computer mainframe). Thinking of Lister's first encounter with Holly in Red Dwarf, he sees an opportunity to clean up if he ever gets Home, and asks HEX for the winners of various football championships and big horseraces that are yet in his future. HEX haughtily replies that to give this information will establish a very big temporal paradox and make the Roundworld Project even more unstable. HEX also adds that it is not the destiny of William Hill and Sons, nor indeed any other firm of bookmakers, to be cleaned out if Holtack ever returns to Earth. Holtack also inadvertently assists in making the events of the film Alien terrifyingly real on the Discworld - a place where magic makes imagined things real, and the force of Narrativium turns Roundworld imagining into Discworld reality. He also introduces Mme. Deux-Epees of the Assassins' Guild to the delights of French cinema, whilst speculating on whether she reminds him more of Bardot, Emmanuelle Beart, or Catherine Deneueve, with a splash of Annie Girardot at her most impish. Read the story Slipping Between Worlds here.
In the Discworld and The Big Bang Theory crossover fic The Many Worlds Interpretation, Howard Wolowitz is appreciatively reading press releases from the British nuclear power agency, which smooth over and minimise various little accidents which have occured at power plants owing to engineer error. Howard, a man who is no stranger to engineer error himself, recognises the work of a master craftsman and vows to make friends with PR journalists and press spokesmen, as a sort of professional insurance policy. He also speculates that this guy Terence Pratchett would be awesome if he ever got round to writing science fiction. Howard is slightly dissappointed to find Pratchett hasn't realised this - yet. note This was indeed Terry Pratchett's day job before he started writing novels full time. He claims he was releived to have got a gig writing more life-affirming works of complete fiction.
Notably averted in Empath: The Luckiest Smurf. Peyo is still the creator of The Smurfs in this universe, only the details of how he would come up with the idea of the Smurfs is different, based on a certain artifact that Handy and Empath have created in "Days Of Future Smurfed".
Discussed in the The World of the Creatures, where it's noticed that - despite many fictional characters such as Buffy Summers and Batman existing - Stephen Colbert exists as himself, and not as his television alter ego. The possibility that the alter ego does exist elsewhere in the world is hinted at.
Averted in The Student Prince, a Merlin fanfic; the legends of King Arthur exists in this universe. It's implied that this fic is set in the same universe as the show, although there are some inconsistencies with canon since it was written before the show finished.
A popular fic series for Glee known as The Donutverse includes the "real" Adam Lambert as a character. Imagine the confusion when Lambert starts playing a character on the show...
Mostly averted in the Emergency! fic "Double Fantasy". John Gage is surprised to find out about Bobby Troupe, Julie London, ect in the "real" world, and they don't appear to exist in the Emergncy-verse as they did in reality. "Route 66", Troupe's best known song, exists, so he may in some form, or it may have been written by someone else. Randolph Mantooth doesn't seem to exist there either, as it's only in "reality" that Gage gets mistaken for him.
In Emergence, Team RWBY ends up in the real world. Some of the people they meet wonder how they can exist; and if they hail from a parallel world that the show reflects. The CIA gets recordings of Yang Xiao Long and comment that her voice print matches Barbara Dunkelman, her actress. Later, when Weiss is playing Call of Duty, one of her partners says she sounds like Kara Eberle, her actress.
In A New World, there is no Warcraft franchise, but a game called "World of Warhammer" is mentioned by two Marines when they first enter Azeroth.
In one Blue Bloods fanfic, Jamie Reagan gets shot while taking down a robbery crew. When the police are interrogating the captured robbers, trying to find the one who got away, one of them describes the leader as looking like Bane from The Dark Knight Rises. Jamie's actor Will Estes makes a brief appearance in The Dark Knight Rises as the rookie patrol cop that shoots Batman's EMP device during the getaway from the stock exchange robbery.
In one crossover fic with Supernatural and The Blacklist, the Winchester brothers work with the FBI Task Force to find a demon on Red's list who's been possessing public servants. Prior to starring in The Blackist, Diego Klatenhauf appeared in the Supernatural episode "Croatoan".
In Chapter 22, Sarah and Foggy have a conversation in which Sarah references Law & Order. One hopes they didn't ever watch Criminal Intent and notice that Robert Goren looks a lot like Wilson Fisk if he had hair.
In Chapter 11, when Matt asks Sarah if she'd ever used violence before attacking Ronan, Sarah replies, "Uh...in seventh grade, I slapped a high school boy for telling my friend that her haircut made her look like James Spader." James Spader was the voice of Ultron in Avengers: Age of Ultron.
In Chapter 26, Sarah mentions seeing the movie Noah, a movie which features Anthony Hopkins (Odin from the Thor films) as Methuselah. While that movie's director Darren Aronofsky has worked with MCU actors like Natalie Portman, Mickey Rourke, and Marisa Tomei.
Game of Thrones is referenced on one occasion. Finn Jones (Danny Rand from Iron Fist (2017)) is in that show as Loras Tyrell, as is Jessica Henwick (Colleen Wing) as Nymeria Sand.
At one point, there's an article shown in the Bulletin about the breakup of Ben Affleck and Jennifer Garner's marriage (which happened in 2015, around the same time this work was first published). Affleck and Garner were Matt and Elektra respectively in the 2003 Daredevil movie.
Breaking Bad exists in the MCU since Turk Barrett describes Mysterio as "the latest Walter White wannabe with a stupidass costume” when grilled by Frank. Krysten Ritter, who portrays Jessica Jones (2015), had a recurring role in season 2 of Breaking Bad as Jesse Pinkman's girlfriend Jane Margolis. And Jessica Hecht, who played Walt's ex-flame Gretchen Schwartz, appears in an episode of Jessica Jones as Audrey Eastman.
When Foggy first learns that Matt is sorta-working with Frank Castle, he likens Frank to Travis Bickle from Taxi Driver. Robert De Niro, who plays Travis, co-starred with Charlie Cox in Stardust (Cox as lead protagonist Tristan; de Niro as the secretly homosexual captain of a flying pirate ship).
In Being Female, the infamous sequel to the infamous Becoming Female fanfic, Uncle Vernon is portrayed as a "Christian fundamentalist". At one point, he is reading Chick Tracts and he says aloud, "I wonder how this Chick guy has heard of my nephew Harry Potter?"
Played for laughs in The Flash (2014)/Supergirl crossover Call Me Kara when it's shown that Melissa Benoist exists in Supergirl's universe by mentioning that Alex was attracted to her, bringing up all the shows that Melissa Benoist has been in.
A surprising number of Harry Potter fics avert the trope by having Harry meeting/mistaken for Daniel Radcliffe or vice-versa. In one Harry/Snape fic the two of them spend several nights watching Alan Rickman movies.