Ai Yori Aoshi Koi: Chapter 8 reveals that in the past, Kaoru's aunt Suzuno actually drugged and raped Kaoru's father to conceive a child as part of a plan to become the Hanabishi heir. Yeah, it's just as f'ed up as it sounds.
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.
The Dark-aligned pureblood families are a popular target as well, and not without some justification; between the apparently quite small population of magic users in the UK and their obsession with eugenics and blood purity it's actually rather plausible.
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.
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.
Bart and Lisa get a lot of incest fics. One in particular had them fall in love, marry and have a daughter together, living under assumed names in another town.
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.
Ed and Al are a surprisingly popular pairing in Fullmetal Alchemist fanfiction, likely because the 2003 anime really went to town with the Incest Subtext, intentionally or not. Ed and Al seem to be a little too obsessed with each other for it to be merely brotherly love.
From Gravity Falls, the Dipper and Mabel pairing (also known as Pinecest) is very popular, with several fanfictions having been written for the pairing.
In a side story of A Brief History of Equestria, one of Platinum's plans was almost derailed when it was revealed that one of the kitchen staff of the noblepony she was having done in was pregnant with the grandfoal of the Noble in question. However, said maid was also the secret daughter of another maid, with whom the nobleman had most certainly sired the younger maid with years ago, leading to this trope. It isn't known whether or not the two younger ponies knew this, or if one knew and the other didn't, but given nature of the Founding-Era Nobility in character and in marriage arrangements, that knowledge may or may not have had any effect on the matter.
Hivefled: The Grand Highblood and the Condesce produced their respective descendants together and have every intention of making them follow in their parents' footsteps; troll society has no concept of incest, but Gamzee is still not happy about it. He has, however, made flirtatious comments to the ghost of their half-sister, but considering his current trauma level nothing was intended to come of that.
One of the most popular pairings in the Frozen fandom is the sisters, Elsa and Anna. Though many writers create AUs in which the duo are not siblings, others choose to focus on how the sisters admit their affection for each other, struggle to deal with the associated taboos and how to present the issue to their kingdom (more than one fic involves the pair being forced to flee Arendelle, temporarily), and balance their royal duties with their sharply increasing sex lives. Usually the affections are mutual; a few fics, though, make it one-sided, creating heaping amounts of Angst in the process.
In The Once and Future King, the main character, Prince Aziru, is the product of incest between Zuko and Azula, who have plenty of Incest Subtext in the original show. Unlike most examples of Royal Inbreeding, the siblings are not married (instead on opposite sides of a civil war for the throne of the Fire Nation), and Azula only chose to have a child with Zuko so they would have pure, strong Royal Blood. Aziru, along with everyone else, doesn't know who his father is yet, and only sees Zuko as the Evil Uncle he has to kill.
It should be noted that it's very unclear whether the sex was consensual, on either side. We don't know anything about how willing Zuko was, and Azula never specifically says she chose to have a child with him.
Seemingly played straight but ultimately averted in the Kim Possible fic "Vacation From the Norm". In the first volume, Global Justice head Betty Director appears to have betrayed GJ and has seduced her brother Sheldon, aka Gemini, leader of the World Wide Evil Empire. In the sequel, it's revealed that Camille Leone was impersonating Betty Director and was the one sleeping with Gemini. The real Betty had gone underground, and was actually romantically involved with Agent Will Du.