There are fanfics where the reader may insert himself/herself in the story with a yandere character. They may be normal characters turned into yanderes, they may be characters who boarder on or could be yanderes. Heck, the reader could be the yandere. Have fun sleeping after reading one of those!
In Ragnarok Takada towards Light. When Light began dating her in college they agreed it would be nothing serious since they both wanted to focus on their careers. But when Light broke up with her Takada did not take it well and has held a grudge for four years and seems to be out to ruin Light's career.
In Do Not Meddle In The Affairs Of Wizards Ginny is a Yandere who stalks Harry to the point where even Yuno Gasai would have been going '... a bit much, surely?', deliberately impregnates herself with stolen sperm and then tries to use the test-tube-child to trap Harry into marriage, and nearly kills Luna for the high crime of talking to Harry (although in fairness the part where Luna almost died was an accident — Ginny didn't know that Luna was seriously allergic to bee stings).
In Somno Veritas Harry finds that the only thing more frightening than Voldemort trying to kill him is Voldemort's infatuation and getting crazy possessive over him especially since Voldemort never learned to handle emotions before he hacked up his soul so he's very volatile going from displays of kindness to violently psychotic at a drop of a hat.
Savannah Carlyle from If You Only Knew. She begins a relationship with Puck and starts to show symptoms not long after her introduction but it is all culminates with her killing Shelby, Puck's ex. She even sings the Yandere song "This Little Girl" by Cady Groves as her confession.
Dani in Changing Directions, is obsessed with Faith, and threatens to rape her, but in this case, her obsession is treated as a disease and she is Put on a Bus to deal with it.
The Condesce is often portrayed as having romantic feelings for the Psiioniic. In canon, she wired him permanently into her spaceship's engine so his psychic abilities could be used as a power source; as the fanworks would have it, it was also so he can't leave her. Referenced in Hivefled, in which the Grand Highblood is also distinctly yandereish towards the Handmaid; he killed her, kept her skull, and painted a portrait of her in her blood.
One of the most common portrayals in the Happy Tree Friends' fanon anime version depicts Flippy - who is an Ax-Crazy, psychotic murderer in Canon- as an Yandere for Flaky. The canon episode Without A Hitch plays with it a bit, because Flippy constantly follows Flaky around, trying to be nice to her, while she is so terrified of him, that she tries to get rid of him at all costs.
Ultimate Re Imaginings gives us Natasha Romanov. She tried to kill Joey and blatantly implied she's the one who got Clint's family murdered. And when her attempt to kill Joey backfired the first time she framed Clint before ultimately trying to kill him too because he was spending too much time with Joey.
And this is to say notihng of how Andrea Rourke is turning out from her previously innocent protrayal as Joey's Shrinking VioletTsundere Type B friend. And as of 'Over The Edge,' she's officially proven just how fatal her love is. Even more disturbing is that when Joey returns from being kidnapped again he's going to be in for a nasty surprise.
At first, Ronald Hilliard turned himself into an electricity-spitting monstrosity and began murdering Spider-Woman's critics as a way of displaying his affection for her. When, Ronald, now calling himself Supercharger, professes his "love" for Spider-Woman, she disgustedly points out that she can do without the "love" of a sick freak like him. The resulting Freak Out leaves Supercharger torn between his obsession with making Spider-Woman his girlfriend and his obsession with torturing and killing her for "rejecting" him.
Admiral Daro'Xen, the Big Bad of Project Gethinator, is crazy in love (or is that lust?) for Commander Shepard. She's gone into quite in-depth study of Shepard's history and psychology and has determined that Shepard is quite susceptible to the charms of female quarians, and nothing will dissuade her from the notion that she and Shepard were meant to be together. Everyone else working with her (particularly her second-in-command, Hvenna'Tor) considers this aspect of her to be utterly disgusting. It definitely doesn't help that she's written a collection of Self InsertReal Person Fics about herself and Shepard, with a reputation for depravity second only to that of Fornax's Forbidden Issue. When she and Shepard finally face off in the final chapter, when Shepard turns Xen down (because Xen is completely out of her mind and because Shepard is in love with Tali), Xen has an If I Can't Have YouVillainous Breakdown of star-system-shattering proportions — she turns the same mineral scanner that Tali's idiot crewman Prazza (who was responsible for the Forbidden Issue being labeled such) accidentally blew up a star with in the very first chapter of Inglorious Boshtets on Eta Carinae, causing it to go hyper-nova in a furious bid to destroy Shepard, Tali and the entire Normandy crew.
Played for laughs in the rather bizarre story, ''Stealing the Deed'' when it seems that Trixie has become a very strange and desperately in-denial version of this. Just about everything she says in this story is either filled with unadulterated Insane Troll Logic, or both confirming and attempting to deny her yandere-ness.
Hilariously, Shinji Ikari for Kaworu Nagisa in Playing With Fire, who tries to force Kaworu to complete Instrumentality so they would be together forever. Shinji blames this on Kaworu for being the only person nice to him. (Maybe it wasn't a good idea to only person to be kind and openly loving to the person you need to kill you.) This ironically causes Gendo to realize that Shinji is truly is his son.
The Simpsons fan-created character Mara Morrigan, originally from unfinished fanfic "Bart Simpson's Obsession" but since then appearing in other works by various fans, is the sweet-seeming but secretly Ax-Crazy cutie with an unrequited love for Bart. The original fanfic was supposed to have ended with him having her committed to an institute to save his own life.
Vicki in The Jill Gilbert Saga is very violent towards Jill, even more so when she becomes a vampire. Jill has hints of one herself and fully becomes one when Klaus tells her turn off her feelings that don't involve him.
Yukari was a maternal one in Mine towards Reimu, who is, at the time, about one and a half years old (ergo, an infant), and was more than willing to take Reimu to the grave with her, literally. Her reason for this was because she was Reimu's wet nurse and, in breastfeeding her, grew attached and didn't want to give her back to her birth-mother (the then shrine maiden), as she's cared for her since birth and sees herself as being Reimu's mother, ergo she is more than willing to kill herself and Reimu, too, just to keep 'her baby' from being taken from her, making her Type 1: Possessive. However, she is a mild one as she would have only killed herself and Reimu too as a last ditch effort but her willingness to do it at all shows her attachment and exactly how unwilling she was to let Reimu go. Of course, she only said she would but, if she fled and Ran still continued to chase her down further, it would be likely she would have gone through with it or fled to the Outside World, though the former is more than likely than the latter.
Definately played to a minor maternal sort in Touhou MAMA, a crossover of the Touhou Project and the film Mama where Yukari, playing the role of Mama/Edith Brennan actually does take Reimu to the afterlife with her just to keep from losing her, with Reimu, playing the role of Lily, happily going with her "Mama". As a matter of fact, when Reimu is taken to be with her family, Yukari decides she wants none of it and is not going to allow anyone to take her 'child' away from her without raising hell first, thus it escalates to her spriting people away and causing Gensokyo to descend into a panic over the events.
Claudia Bartlett is one you would never expect. At first seeming like an inhumanly stoic character with Mrs. Robinson vibes, her affection for Matthew seemed purely superficial and based on his physical attributes. She does not really care that she is his teacher, only that her husband - an insurance manager - is never around to "take care of her needs". It turns out Claudia is madly in love with Matthew...because he looks like Dad, who she's had sex with previously. She tries to drug him with Rohypnol in the victory party over Nebiros, and comes very close to molesting the poor guy. She then becomes convinced she needs to kill her husband for him to love her.
Much more maniacal is Joshua-Antonio, who has a Psycho Supporter thing going for Nebiros. He "does not want anybody but Matthew to challenge Nebiros", viewing his service as basically an act of love, and serves Nebiros not for a vendetta against society or against certain sub-cultures, but because he genuinely loves his boss. Nebiros being a deformed Monster Clown has not impacted this in the slightest. He actually becomes very, very angry when Wayne Reverie speaks badly to Nebiros.
And the last is Katherine Daille. Consider that she is actually mentally ill, mostly caused by positively hideous abuse by her father and brother. Matthew was the only "steady thing" / "safe thing" in her life, and he defended her many times from bullying from school boys all the way into high school. As a result, she became hell bent on trying to secure her position as his girlfriend so she can get out of her house and get into his. She rapidly mentally declines as more women enter Matthew's life "threatening her love" or so she thought. She is a very sympathetic Yandere, but also the most unstable one in the book. It probably doesn't help that her Spell Core power involves summoning horrifying demons that exist to kill people...