- In Eva fanfiction, the Peggy Sue fic is extremely common, the most well-known being the doujin RE-TAKE. There are also fics out there that set up a For Want of a Nail situation, and then reveal that either the changes were actually caused by a Peggy Sue or some type of Eternal Recurrence situation. There are also Crossover fanfics with a Peggy Sue. It's reached the point where some fans think that Rebuild of Evangelion is one of these!
- Post-Third Impact fic. This can range from Shinji and Asuka by themselves in a wasteland, to everyone coming Back from the Dead and the world returned to (mostly) normal. Most of the time, Rei has vanished and Toji gets his leg back (both of which might be supported by canon).
- Fix Fics that work by making the setting Crazy Awesome. This was started by Shinji And Warhammer 40 K and continued by Nobody Dies and Mobile Fighter Evangelion. The controversial Neon Exodus Evangelion might be considered an Ur-Example. Some people thought Rebuild was an official version... until 3.0 came into the picture. There is a mini-genre of Evangelion
- There have been several stories involving Shinji being raised by someone other than his uncle/teacher and exploring the For Want of a Nail aspect of how Shinji's personality changes. Sometimes Shinji gets raised on a product, like the aforementioned Shinji And Warhammer 40K.
- Reincarnation fics, especially Kaworu/Shinji Reincarnation Romance. As well as explaining how the different canon continuities are related to each other, this gets rid of the pesky "Kaworu is an Angel" problem. They are especially popular since the third movie of Rebuild of Evangelion.
- Fusion Fics where the crossover element provide a well-needed Level In Badass to one or more of the cast members, providing him/her with the tools to make some real change on the situation (sometimes it's probably something as simple as the "Crossover Element" giving them a Dare to Be Badass speech-still, the "nail" in the "For Want of a Nail" that the fic covers came from elsewhere). While this is covered in some of the examples above, this has also been the drive behind some stuff like a minor niche of Evangelion Super Fic stories (example: the Superwomen of Eva series, Last Child of Krypton, Shinji Ikiryo, Thousand Shinji, Children of an Elder God), and one of the "Crossover Element gives pep-talk to Eva character" examples would be that of Series Thirty and Three Quarters (or "Shinji And The Doctor").
- More Evangelions existing; sometimes just as a platform to have an Original Character as a pilot (or making one of the canon characters a pilot, like Kensuke for instance), sometimes to explore the political and personal ramifications of having to go to war against another country with an Evangelion (this became somewhat-canon on the Rebuild of Evangelion films).
Fandom Specific Plot / Neon Genesis Evangelion