In the Death Note fic A Cure For LoveLight begins a relationship with L during his Memory Gambit but when Light becomes Kira again he becomes very possessive and obsessive of L. He begins making up excuses to himself why he isn't going to kill him now like "it's not a good time," or "I want to break him first" (suggesting he really does love him underneath the psychosis. Light becomes very angry and upsetwhen someone else tries to kill L.) Light arranges things so that Misa kills Watari, and then he kills her because he felt threatened that Watari was going to make L break-up with him and that Misa (a Yandere herself would try and kill L so that she and Light could be together). Light keeps L drugged up for weeks afterwards and spends so much time with him that his infatuation becomes rather obvious to everyone at which point Light even considers killing his own father because he's against their relationship. Later when L in effect breaks up with him, Light goes completely off the Morality Chain. He uses the deaths of his father and a former teammate to essentially takes over the world in an afternoon.
SMG4 Bloopers: Saiko Bichitaru is in love with Fishy Boopkins...and is shown to be as psychotic as her name implies. Of course, being a comedy series, this tends to be played for laughs to a certain extent. She later joins the cast of the protagonist and becomes somewhat of an anti-hero, similar to Mario himself.
Admiral Daro'Xen, the Big Bad of the Mass Effect fanfic 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 literally 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.
In RagnarokTakada 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.
How I Became Yourswants us to believe Mai is this after Zuko dumps her for Katara, but the truth is Mai was nothing but a patient woman who stood by her husband and tried to protect him from scandal, no matter how hurt she was that Zuko was basically cheating on her with another woman. In the end, it's Katara who ends up being the yandere when she kills poor Mai in cold blood to keep her away from Zuko.
Cori Falls's fics portray Jessiebelle as a yandere for James, to the point where she outright tries to murder Jessie in one of them.
One sporker interprets James as a yandere due to his obsessive, creepy hyper-focus on his and Jessie's romance and the endless desire to cure her angst, complete with swearing revenge on anyone and anything that upsets her. (Usually Ash and his friends)
Akira Kogane/Keith is a borderline case of this in the Voltron: Legendary Defender fic Across the Multiverse as he chases Takashi/Sven/Shiro through every single Voltron incarnation and spits venom at anyone who dares get too close to "his" man. Especially poor Curtis.
Detractors of Edelgard in Fire Emblem: Three Houses like to portray her as this towards Byleth, especially the female version. This is especially popular in Dimitri/Byleth fanfics due to the pairing's popularity and many Dimitri fans being Edelgard's strongest haters.
Dimitri himself can become this towards female Byleth in either Crimson Flower or in fics meaning to make his post-timeskip "feral" self look even worse for the sake of drama.
Quotes • 
Headscratchers • 
Playing With • Useful Notes • 
Analysis • 
Image Links • 
Haiku • Laconic