In Chapter 77 of Hottie 3: The Best Fan Fic in the World, which involved fusion, all three Crystal Gems fused into one being. A few months later, the Steven Universe episode "Giant Woman" aired on TV and established that Gems have the ability to fuse with others. Even better, they all eventually did fuse together in a later episode.
Kara Zor-El and Dev-Em become lovers. Flash-forward several years and Dev-Em is one of her enemies in the main universe and the DCEU.
An alternate universe Saturn Girl is brunette, right like Supergirl's Imra Ardeen.
Kara having a Legionnaire lover who wants her to move to the 31st century with him, several years before the Justice League Unlimited episode where Kara fell in love with Brainiac 5 and moved to the Legion of Super-Heroes future.
Satan Girl planning to force entire worlds to worship her like a goddess several years before Supergirl's Sterling Gates' run reimagined the character like a death and love alien goddess.
A Kryptonian doppelganger of a hero of the House of El plus Mordru plus the Legion of Super-Villains come together to destroy the Legion? And the Supergirl of Earth-One gets to do some fighting? It kind of sounds like Final Crisis: Legion of Three Worlds which came out nine years later, isn't it? Compounded by the fact Darkseid was the next Big Bad.
Kara isn't sure what she wants to join the League. A few years later, Supergirl would join the Justice League in the comics.
HERZ: In chapter 4 Asuka calls her daughter Akiko Aki-chan. Several years later, when Jimmy Wolk was writting The Second Tryhe named Shinji and Asuka's daughter "Aki-chan".
Avatar: The Last Airbender fanfic The Stalking Zuko Series has tension growing between the Northern and Southern Water Tribes, with North viewing the South as uneducated yokels and the South view the North as stuck-up busybodies who didn't lift a finger to help them when they facing genocide from the Fire Nation. Then Season 2 of The Legend of Korra comes out...
The GleeGender Flip story, A Different Direction, has Faith (female!Finn) complaining about Lebron James leaving the Cavaliers in 2010; a few months later, Lebron would return to Cleveland.
In Chapter 7 of Necessary To Win, Yukari infiltrates Anzio, which, instead of Saunders, is Oarai's first opponent. In the Anzio OVA, she ends up infiltrating Anzio as well, but unlike in the fic, doesn't get caught.
Tara Gilespie, author of the most infamous Harry Potter fanfic of all time, predicted in an author's note before Deathly Hallows came out that Harry would have to let himself die in order to defeat Voldemort, because he himself is a Horcrux. Fast forwards to when the book came out, and she was right! A lot of people had the same idea, to be fair, but the fact that Tara of all people figured it out is hilarious.
The Vampire DiariesGender Flip story, 'The Sara Diaries', features Stefan as a girl named Sara Salvatore. In Season Six, it was revealed that there actually was a Sarah Salvatore, Zach's long lost daughter.
Said story also predicted that Stefan and Damon's mother is still alive.
Weiss Reacts: The fic featured the Humongous MechaGurren Lagann as a regular plot element, had Jaune crossdressing for a Saber cosplay and Cinder joining the school as a teacher. Months later, the Atlesian Paladin is unveiled as a regular plot element of Volume 2, Jaune ends up crossdressing to cheer Pyrrha up, and Cinder ends up in Beacon as a student.
Similarly, plushies of Weiss are a Running Gag- and one Ensemble Darkhorse, Vivi, is an animated Weiss plushie. Now that Rooster Teeth have actually started selling Weiss plushies....
Back in 2001, an author named Kanius did Digimon Fusion (Digimon characters play the roles of DBZ) and is doing a remake called Digimon Fusion Kai around 2010. Comes 2013, that the english version of Digimon Xros Wars is titled 'Digimon Fusion'.
Somewhat an inversion of ascended fanon. The English dub version of Guilty Crown in the final episode's epilogue, the casts last words are "To the New Year!", then co-authors are doing a mega crossover fanfic based on New Years Eve.
Then plays straight in other parts. In Chapter 8, Captain Ginyu mentions his thanks of Freeza getting back his own body back. I wonder what happened officially in Dragon Ball Super?
Chapter 1 has Kirito mention himself being Samurai Jack, alongside the Minions of Set appears and Arago's super form looks like Aku. Then, Adult Swim renews the cartoon for 2016.
Chapter 32 shows the The Powerpuff Girls (2016 versions) siding with the Green Lanterns (John Stewart, Razer, and Aya). Promos of the PPG reboot shows the girls creating similar constructs.
In episode 32, a Spaniard Pretty Cure explains that there are other Pretty Cure teams around the world. A few years later, that would become canon.
The main character of this fan fic is named Chloe. As of 2015, Smile Pretty Cure! is being dubbed as Glitter Force, and one of the dub names revealed is Chloe (but the Chloe in question is Reika/Cure Beauty).
The first completed Naruto fic on FF.net was a Naruto/Sasuke fic (in fact many early fics were). It ends with an author note that says "More Naruto fics, I think, are needed". Within six years Naruto would be one of the biggest manga fandoms and is only behind Harry Potter as the fandom with the most fanfics on the site.
This fanfic crossover has Ben Tennyson and Yang as acouple and they get along pretty well. Volume 3 arrives and Ben's voice actor, Yuri Lowenthal, is now the voice of Mercury Black and he and Yang are enemies. What makes it hilarious? The fanfic came first before volume 3.
Its version of "Ghost Godzilla" from All Monsters Attack was illustrated using a purple atomic breath. This ended up being the case in Shin Godzilla.
Early on in the story, Mothra Lea's changeling form is called a "rainbow changeling" as a joke descriptor because of how unlikely it seemed given the species is dark colored. Three years later in Season Six of the show and we ended up getting actual rainbow colored changelings.
The Bridge's King Sombra is an abnormal unicorn composed of dark magic, having a direct hoof in the "death" of Princess Amore, being able to hide in crystals; and coming back to life via dark magic and his surviving horn. IDW Comic's King Sombra released months later had all of these traits.
Before his death, Jim Bader was going to make Ranma and Nabiki’s next child in A Very Scary Thought be an Expy of Erza, this time with Nabiki as the Fama and Ranma as the Ouma. When Erza’s mother Irene Belserion is finally revealed she is a voluptuous redhead who used to be known as the Dragon Empress. To be more specific Ranma’s ability comes from forming a pact with five Elemental Dragons.
A fancomic for The Loud House featured the Loud siblings, over the course of the comic, cosplaying as various different Nickelodeon cartoon stars (Lincoln as several male leads and Leni as Patrick Star for example) but the one that's this trope is Luna. Her cosplay is being stylized to look like Sam Manson, who turns out to share the name and gender of Luna's ultimate crush.
The training Ranma gave Vegeta in Human Saiyajin is pretty much the same training given to him by Whis is Dragon Ball Super. I.e showing him how to overcome the DBZ universe’s Unskilled, but Strong approach to martial arts by training him how to better control his ki and body.
In the House fanfic "I Am Not The Walrus" Chase inadvertently admits furries make him nervous, which House finds hilarious, sarcastically asking him if he was "ravaged by a herd of My Little Ponies". This was written before My Little Pony: Friendship Is Magic existed.