I won't be able to name all of them because I read so many over the years I lost track, but here's a list of some of the fanfiction I've read-
D.O.L.L. (Codename: Kids Next Door)
This fanfic, far as I know, was never finished, and it is a shame too. The story, although no longer canon with the series, really explored the psyche of one of the Delightful Children From Down The Lane, who, previously, have been shown to be so obedient and well-mannered that they didn't feel like human beings anymore. The story involved one of the girl members getting separated and is taken in by the KND, where she begins to show signs of her own personality and awareness of self, and Father, the main villain and caretaker of the Delightful Children From Down The Lane, doesn't like it.
Land Beyond Time (Land Before Time)
This was one of the first long LBT fanfics I've read and remains one of my favorites, despite it not being online (it was removed due to it being in script format) for years. The story had plenty of action, convincing integration of advanced technology in the LBT world, twists and turns, great characterization, and emotional conflicts. The story had a few subplots melted into it, 3 of which included Ali joining the bad guys after she is tricked into thinking Littlefoot killed her mother, a flightless and vengeful Pterano attempting to get revenge on those whom he believe wronged him, Petrie finding out his uncle is really his father and his father was really his uncle, and Shorty being turned against Littlefoot through a painful mental device that magnified his resentment towards Littlefoot and Bron's father and son relationship.
Son of Scar (The Lion King)
Released before The Lion King II, Son of Scar told the tale of a very big (even bigger than Simba) dark lion named Kisasian (I might not be spelling it right). It was extremely long, but also an enjoyable read. The story involved Simba having to contend with Kisasian, who wants revenge against Simba for killing his father. Kisisian is portrayed as a cruel character, even not treating his lionesses right (two of which actually abandon him to be with Simba). Kisasian is nothing like Kovu and more menacing than Kovu was when he was still brainwashed by his mother. The story was quite violent, particularly when Kisasian rips Simba several times to the point where he could barely move. Although revenge fanfics involving the offspring or sibling of a character aren't that uncommon, back then it was something new that I hadn't seen before and the author really pulled it off well in my opinion.
Beyond the Other Side (Digimon)
One of the best fanfics I've read for this fandom, Beyond the Other Side crosses over Digimon season 2 and Digimon Tamers, and yet somehow manages to keep many key elements canon to each show in tact. The interactions between the two sets of characters is intriguing, even conflicting at times, such as how Rika kills Digitamamon and has Renamon absorb his energy, which enrages Yolei who says that he could have been saved if the dark ring was removed from his body. The story still retained the formula of the series, in my opinion, but also introduced elements that would otherwise not exist in the shows, one of my favorites being when the DigiDestined find out that, in the Tamers' world, they are just fictional characters. This brings about a rather emotional sequence and the author managed to portray this sequence without it becoming too over the top or crazy.
Twisted Reality (Code Lyoko)
This is probably one of the darkest, if not the darkest, Code Lyoko fanfic I read. It involves Yumi going into another world where XANA is terrorizing the Earth, accompanied by Jeremy. While the story does have its share of action, the real focus of the story, where it truly shines, is the psychological aspect of it, like how the alternate versions of Odd, Ulrich, and Ayeka are affected by Jeremy's portrayal and how they react to the good Jeremy and how sadistically cruel the evil Jeremy has become and how he constantly likes to torment his former friends. If you want to read a fanfic that has a lot more psychological conflict, this would definitely be something I'd personally recommend.
