The Script FicCalvin & Hobbes: The Series has a minor example - the episode "Eggs for Calvin!" is first released on a holiday episode compilation DVD before being shown on television proper.
Another Calvin and Hobbes related one is two stories, Calvin And Hobbes Forever and Calvin, Susie and Hobbes. The second is a sequel to the first and the plot revolves around Calvin, now in his 20's is an unsuccessful writer who, with help from Susie Derkins and his old friend Hobbes, begins to get his life together, however, many crazy things happen along the way. Many other comic characters from other comics, such as Riley and Huey Freeman, Ed Wuncler III and Gin Rummy, Garifield and Jon, Jason show up along the way. The first story was finished, however, the sequel and the original story suddenly vanished one day with no trace without ever finishing...
Red Aigh wrote a deleted chapter for the book "The Wind in the Willows" that gave a brief romance between Rat and Mole shortly after meeting then continues on with the rest of the book normally. The author later explained he wrote the chapter in response to several online theories that the main characters (male bachelors that eventually live together) were intended to be homosexual by the original author.
Jewel Of Darkness: When the Titans fight Susano again during the Rivalry Arc, they all refer to an unseen second encounter during the Jump City Arc that ended with a crazy Marine dragging him into another dimension. The author even refers to this chapter as "The Lost Episode", stating it was cut for pacing purposes, and that it'll be eventually published separately.
All The Babysitters Club fanfiction by melcia was deleted and doesn't seem to be located anywhere else online. This is especially bad news for fans of her "Forever" series.
All but half of Cori Falls's Pokemon fanfiction and all of her Yu-Gi-Oh series has been deleted along with her websites, much to the disappointment of anyone who was a genuine fan of her writing (usually for nostalgic reasons) or liked reading her stuff for other reasons.
Due to site regulations, technically making it banned, we cannot read about the warden raping Yukari in Gensokyo 20XXI, though Amoridere did write a chapter about it, as well as a sidestory, The Warden's Lover, that one can read on Mibba, where it is rated NC-17.