A popular The Legend of ZeldaHigh School AU 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 GameCube, a console he himself appears on in this universe.
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.
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.
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.