There seems to be no sign of incest in the original book, but that didn't stop the The Chronicles of Narnia fans. The most popular pairings are Peter/Susan and Edmund/Lucy, with Peter/Edmund and Edmund/Susan all very popular as well. "Blame the chemistry between the actors." As you can imagine, given the Christian origins of the stories, this is a large division for the fanbase.
Thanks to the onscreen chemistry between the actors portraying them, Tru and Harrison Davies of Tru Calling developed a small but dedicated shipper following. One of the better stories (NSFW.
The ever squicky amounts of Maria/Shadow fanfics. There's even a couple that has Shadow raping Maria.
Of course, the Sonic franchise is slightly ambiguous about whether the two of them actually thought of themselves as siblings, depending on the instalment and continuity. And in any case, not only are they Not Blood Siblings, they're different species.
Almost three quarters of the Wizards of Waverly Place fandom prefer Justin and Alex together. On Fan Fiction. net, there are around 3000 stories and more than half are about an incestous/romantic potential relationship between the two of them. The actors and their chemistry didn't help either, as Selena Gomez and David Henriedid use to occasionally date a few years ago.
The most infamous and best voted and appreciated fan story in the fandom is In Fire, In Ice, in which Justin and Alex end up married.
Also squicky in the fact that the OC knew that Diego was her brother all along but still engaged in a semi-intimate relationship with him. Diego on the other hand didn't know until after The Reveal.
D.Gray-man fandom has a somewhat sizable following of Leescest shippers. That is, Lenalee Lee and her big brother Komui Lee. It certainly helps that Komui has quite the sister complex and freaks out every time he's jokingly told that Lenalee's getting married.
One of the threesomes in the Magical Girl Lyrical Nanoha fic A Day in the Life is Ginga and her adopted siblings Wendi and Nove. Genya ultimately ends the relationship by having Ginga reassigned, though, but the three of them say they will take the time to think about their feelings for one another.
In Lisa Is Pregnant, Bart and Lisa are trapped on a snowy mountain, and Bart has sex with Lisa in order to warm themselves up. Bart dies after exhausting himself, but Lisa survives, and is pregnant with his child. She wants to abort the baby at first, countering Marge's suggestion that it's all that's left of Bart by saying that it's her body and her decision, but decides to have it out of respect for Bart.
In the Oneiroi Series (one of the few Order of the Stick fanfic series), Deirdre has a 'thing' for men in her family. She deliberately puts Terentius in a position where he can't help but confront and nurse lust for her, which is torturous enough for him to break down in tears, once when he masturbates to her and again when she actually gets him to do the deed. Deirdre's not a nice sister.
Decadent Habits features quite a few people discovering that they are actually half-siblings and then having sex anyway, as well as a few where only one party (or neither) is aware of the relationship. Pairings have included Setsuna/Konoka, Negi/Asuna, Negi/Ayaka, Ayaka/Chisame, Negi/Chisame, Negi/Nekane (who is also his real mother), and Ayaka/Nekane as part of an Ayaka/Nekane/Chizuru threesome. Sex is also vaguely implied to have happened between crossover guest stars Itoshiki Nozomu and Itoshiki Rin. So far, the only newly discovered siblings who haven't had sex are Haruna and Satomi ... though Satomi indicates that she wouldn't mind ...
Golden Sun Gag Battle, a 4koma doujinshi, has a joke with Ivan trying out his new Reveal power on Hama and Feizhi's clothes. To be fair, Gag Battle was published before The Lost Age outed Hama as Ivan's sister.
Golden Sun fandom being notorious for its rampant Shipping scene, there's also the aptly-named "Oopsieshipping" (Felix/Jenna), and "Imilshipping" when it was thought that Alex and Mia were siblings (Dark Dawn since clarified that they're cousins... which hasn't slowed the shippers any).
The first Shipping Chart shown on the My Little Pony Friendship Is Magic fansite Equestria Daily recorded no less than five fics shipping Applejack with her brother Big Macintosh, and another five with the sister/sister pairing Celestia/Luna (Princest). And those are just the ones that made it past the EQD pre-readers.
Considering Fire Emblem has some canon examples, it's no surprise this trope is extremely common among certain pockets of fandom:
The Sacred Stones had a few Tana/Innes shippers.
Shipping the Nohrian and Hoshidan siblings with each other is popular in Fates fandom.
In Three Houses, a good chunk of Dimitri/Edelgard shippers were drawn in by the fact that they were stepsiblings at one time, albeit without realizing it.
Male Alear/Veyle from Engage is easily the most written-about ship on AO3; while many fans jumped ship when it was revealed they were siblings, some fans shipped it even harder for that reason.
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