Dakari-King Mykan always wanted to make a more action-oriented story than Friendship Is Magic, to no real avail. Come the season 4 finale, suddenly the show he hates actually gets an amazing action sequence that blows any he could make out of the water (not like that's particularly hard). Irony at its finest.
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.
Dakari-King Mykan's reasons for creating The End of Ends become extremely laughable when the finale to another one of his stories, Cyborg Davis, has an ending that's exactly like the ending to Things Change. Beat. For. Beat.
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.
In Trolling the League, Naruto and Xanna claim to be highly advanced aliens who elevated humanity millenia ago. In an omake in the sequel Xanna runs into a human who insists gods don't exist and that she must be a highly advanced alien who elevated humanity and/or has come to soften up Earth for an invasion.
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.
This piece of fanart for The Legend of Korra depicts several characters discussing their reactions to fan pairings involving them. Panel 4, where Asami is trying to convince her father that there's nothing going on between her and Korra is hilarious if you've seen the show's finale.
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 Precure is being dubbed as Glitter Force, and one of the dub names revealed is Chloe (but whose name will be Chloe is unknown at this point).
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 fics on the site.