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Sho of Crimson Rafflesia is a Cute and Psycho psychic power user who has a strange obsession with the the male deuteragonist. Specifically, she wants to be the one who kills him For the Lulz, and heaven forbid anyone who tries to get in her way, even the de facto government.
Sakura of Da Capo is very, very dere towards Junichi but as the story continues, psycho personality traits emerge more and more frequently, starting with the implication she dropped a tree branch on someone's head because they mistook her for the lead's younger sister and treated her like a kid. She gets worse, both in back and mainstory.She can't really help a lot of it as stuff just happens when she thinks about it.
The ending to the anime, though, is a straight example: the pregnant Sekai stabs the lead character Makoto to death, and her rival Kotonoha later kills Sekai and cuts a hole in her body to see if she was pregnant at all, then cuts Makoto's head off and leaves with it on a NICE BOAT.
The manga changes it. Sekai kills Kotonoha and Makoto doesn't die.
In the Visual Novel game Tsukihime, there's a rather chilling example of a less romantically inclined (at first, that can change depending of your choices) Yandere coming completely outta left field the first time you notice it. Spoilered because it will ruin a lot of the Far Side of the Moon stories: The seemingly cute and funny meido Kohaku, who underneath her cheery facade has managed to kill all her emotions (effectively becoming an Emotionless Girl), experiments dangerous drugs on people without losing the smile, and is plotting the extermination of the family she's serving because of the abuse she had to go through as a kid. If you pick her and her to come to grips with herself, your sister Akiha then goes insane. Apparently insanity can not be destroyed, merely transferred.
Satsuki "Sacchin" Yumizuka. After she becomes a vampire in the Far Side routes, she sucks the blood of the innocent... mostly to survive, but also so that she can understand Shiki's "scary side" and be with him forever. When he refuses, she attempts to make him one of her brainless minions. Yikes.
An odd example is Roa, who'd spent so much time devoted to his research, he failed to recognise his own obsession with the White Princess, even as he tricks her into drinking his blood, bonding them forever, and at the same time sending her Axe Crazy, causing her to kill her handlers and giving her the freedom to choose her own life.
Everyone but Shiki, Hisui and maybe Ciel. Arcueid? She's damn scary in Ciel's route. Ciel? She tries to set up a sort of double murder/suicide plot with Shiki, but ummm that's her own route so lets say she mostly copes. She gives up completely with only mild hints of how she feels/her backstory in Arcueid's route. Akiha? Goes from Clingy Jealous Girl throughout the game to as scary as Arcueid in Kohaku's route. Kohaku? The final straw in her utter craziness is Shiki's failure to recognize her as the girl at the window who gave him the ribbon. Roa? The last 800 years of his history and Arcueid's backstory is actually because he loved her. Satsuki? Isn't it sad?
Even Shiki isn't safe from being a Yandere — at least, not his Nanaya mode, which actually got off from murdering in the girl who would become the canon victor of their little Love Dodecahedron. It got so bad that, it's very possible that after slaughtering a whole bunch of Dead who were assaulting her, on the grounds that only he may violate her, he actually rapes her (if you choose). Arcueid rationalizes it as him being accidentally caught by her Mystic Eyes of Enchantment, but in reality it's actually a last minute dialing down from outright murder.
Ilya from Fate/stay night is both Possessive and Obsessive on the main protagonist, specially when you refuse to become her living doll/familiar, openly saying she is going to kill Saber and Rin, and to kill the protagonist in the most painful way imaginable.
Limit Panic, a yuri visual novel where both of the potential girls are this.
Zareh from Frozen Essence becomes this if you reject him on his path. More specifically, he seals Mina's powers away and keeps her as a virtual prisoner in her bedroom to prevent her from leaving him.
Lucan from (P)lanets is easily the nicest guy in the game, and adorablybashful to boot. However, it turns out there's a reason for him being the only love interest Marin can get a bad ending with. Namely, he's so fearful of being alone that he unconsciously brainwashed the girls around him with his Mind Control power into becoming obsessed with him. He didn't intend to do this, but if Marin rejects him when she learns about this, he intentionally uses his power to brainwash her into mindlessly loving him. Beware the Nice Ones, indeed.
Charlotte "Charlie" Brontë in Shikkoku No Sharnoth. Apparently, she couldn't bear the thought of parting from her best friend Mary Clarissa Christie someday in the future and thus knowingly meddles with Sharnoth, nearly causing absolute catastrophe and Mary's death at numerous points. All so that ‘tomorrow’ would never come and she would never have to be separated from Mary.
In the sequel Holiday Star, Ryouta himself shows signs of this toward the human girl, and will willingly join The King if he becomes convinced that she likes Nageki more. Sharp contrast with his normal behavior...
Shion Sonozaki from Higurashi: When They Cry, whose Start of Darkness involved her old crush, Satoshi, and her feelings of abandonment when he "transferred." While she's more or less normal in several arcs, the ones where she does snap tend to be some of the most disturbing in a show that has a Nightmare Fuel page to itself, and in the last arc, where everyone's sane she gets very, very... intense when she finds out where Satoshi is.
Rena may count as one for her father. She doesn't harbor any "romantic" feelings for him, but she does love him enough to kill his gold digging fiancée.
Umineko: When They Cry gives us Battler's stepmother Kyrie Ushiromiya. Being a huge Yandere actually saved her life in the duel with Leviathan of Envy. When Levi tells her how she envies her sisters for being born faster, Kyrie just says "So you envied your sisters for seven days? Okay, that's fine and dandy. But what about me? I envied some bitch for eighteen years for being the wife of my man! HOW IS THAT?!" and shoots Leviathan dead. In Episode 6, she tells her niece Jessica in that if Battler's mom Asumu didn't die on her own then she would have just killed her, all to be with Rudolf.
"No, her death was a predetermined fact. If she hadn't died, I would have killed her. The miracle was that I didn't have to stain my own hands."
As a subversion though, in Episode 7 she doesn't give two shits when Rudolf dies, and has no qualms about abandoning her six-year old daughter to enjoy her new freedom.
How about Lambda and Bern? There we have a relationship of two Yandere.
Beatrice: "Fufu… you two really are close, are you not?" Lambdadelta: "… Yeah I like Bern. I even love her. I would like to gouge out her eyes with a spoon so that they can see no other than me."
EP 4 (Kinzo's test) and EP 6 leave hints that George might be such (possessive subtype) towards Shannon.
Kinzo is an absolutely horrifying one, going so far as to rape his daughter who he thought of as a reincarnation of his dead love.
There's an obscure Japanese Visual Novel that's actually called "Yandere", and it's recently received an English patch. The protagonist, Subaru, has three females interested in him: Saki, his childhood friend; Yuumi, his teacher; and Maika, a shy underclassman. The game is called "Yandere" because the females are all in love with him at once, and they strongly dislike each other, and to compound the problem all three possible love interests are psychotic! They start the game with normal personalities, but as you continue to play, Saki starts breaking the chain lock on the front door to come into Subaru's house whenever she wants, Yuumi actually visits the house in the middle of the night to ring the doorbell repeatedly and then repeatedly pound on the door and windows, and Maika keeps visiting the house to move things around while Subaru isn't there. And the endings of this game are all terrible. Here's a list (warning, don't highlight these spoilers if you can't stand really gory horror):
Saki can push Subaru out into the street so he can get hit by a car.
Saki can trap Subaru permanently in a chair by nailing his friggin' hands to it, so she can take care of Subaru for the rest of his life until he dies.
Saki can get hit by a car in the street while chasing Subaru.
Yuumi can take a kitchen knife, stab Subaru to death, and then eat his remains, piece by piece, including his friggin' eye.
Subaru can kill Yuumi instead with a box cutter, and then Saki comes into his house, sees that a romantic rival has been conveniently taken out of the running, and then Saki can eat Yuumi's remains, including Subaru's semen on those remains from an earlier sex act between Yuumi and Subaru.
Maika, who as it turns out is a masochist who loves pain, can stab herself in the stomach with a knife while having sex with Subaru, and then rub her intestinal organs on Subaru...and then, to share the "pleasure" from the pain, she can finally stab Subaru too!
Subaru can accidentally strangle Maika to death during sex after finding out Maika likes pain (he only meant to strangle her for a bit, but accidentally held on too long), and then Saki can come into the house and eat Maika's remains a la the Yuumi example above.
Saki can break into Subaru's house with a chainsaw while he's sleeping, and then use the chainsaw to kill him (Subaru does wake up in time to notice Saki standing over him with a chainsaw, but not in time to prevent her from killing him).
Finally, Subaru can actually get a date with someone else entirely, namely a classical Japanese beauty school idol, but Saki can follow them and step out from behind a tree with a chainsaw to save Subaru from the "wicked woman"...
The game also provides a hidden mini-game of Black Jack (by clicking the block in the subtitle where a k should be). True to form, no matter if you win or lose, you get killed anyway.
Kimimaro Urabe in Sweet Fuse At Your Side is a comparatively mild example, but still counts. He's always softspoken, gentle, and polite - and by the end of the third day, he's made up his mind to do whatever it takes to keep Saki safe, no matter how she might feel about it. This includes making a deal with Count Hogstein, manipulating and deceiving Saki in order to get them both captured and locked up for the remainder of the game, planting a tracking device on Saki by concealing it in his prayer beads and giving them to her as a protective charm, and ultimately planning to sacrifice himself by making the rest of their friends kill him as his part of the deal with Hogstein to keep Saki out of harm's way. In his bad end, he succeeds in going through with it, and it's implied that the reveal shook the rest of the team so badly that they failed the last game and they and the hostages, including Saki's uncle, were all killed by Hogstein as a result.
(Note - major spoilers for several routes.) Makoto Mikami is a more straightforward example: choosing the wrong conversation choice with him doesn't just fail to raise affection - it usually results in him immediately shooting you. This is out of character for both Hogsteing (Makoto) who usually fails to make good on his threats (especially noted near the (good) end of Urabe's route, where Urabe simply walks past the gun-wielding Hogstein in the certainty that the Big Bad won't shoot, and the (bad) end of Mitarashi's route, where despite having the perfect opportunity to kill Ryusei, Hogstein just... shoots him in the foot), and for the game itself, where dying is usually the result of failing a puzzle rather than saying the wrong thing. Makoto's bad end is also the only one in which Saki dies.
In Night at the Hospital, if Frank continually ignores Luka in favor of finding his friend Steve more quickly, Luka eventually leaves in a huff but Frank still manages to find Steve in the end. Except that Steve's eyes change color to Luka's red as he's giving Frank a man-hug. Cue the 'Possessive Ending' credits.
Yandere girls take center stage in Nippon Ichi's rather appropriately named visual novel I Thought It'd Be Harem Paradise But It Turned Out To Be Yandere Hell, where all three of the main character's love interests are violently possessive of him. They even come in different flavors like Clingy Jealous Girl and Stalker with a Crush.
In Under The Moon, an 18+Otome Game, there's two routes for each potential love interest. One is called the "pure love" route, which is typical romance novel fare with fluffy sex scenes. The other is called the "love/hate" route, where the boys become abusively sexy, each falling somewhere on a sliding scale of Bastard Boyfriend Vs. Yandere. All intensely jealous, all afraid that the heroine will leave them, and all prepared to rape and possibly murder to keep her.
Similar to the above example, one freeware visual novel is indeed called Yandere-Chan and involves dealing with one. You can get a good ending, but expect a lot of getting killed for wrong choices. You can get bumped off less than ten minutes in simply for not remembering her name.
Its sequel provides you with two more: Tohru, a friend of the kid who knew your plan, and Akira, who uses you as a torture puppet in one of the game's 7 Bad Endings.
It's faster to list Liar Liar characters who AREN'T Yandere, honestly. Tanaka and... maybe Yukari's ex-boyfriend and childhood friend. Maybe.
In Doppelganger: Dawn of the Inverted Soul, Lee initially appears to be a Nice Guy with an adorable crush on the main protagonist Lucia. Then you find out just how fucked up he is in the head. Like how he drove his last girlfriend insane by murdering a couple of men who were just escorting her home in front of her. And how he orders Raphael, the guy Lucia has a crush on, to break her heart and/or commit suicide in many paths to get him out of the way.
Sora Kasugano from Yosuga no Sora is, in the latter half of her own route, a rare non-evil and non-crazy example. She becomes so obsessed with hertwin brother Haruka that she literally ceases to care about anything else, to the point where she walks out on the porch in a sheet while Haruka is nervously conversing with Nao and Kozue, who have dropped in for a surprise visit, and rudely tells them to leave so that she and Haruka can go back to having sex (in so many words, and more)... The reaction this prompts is about as pretty as it'd be in real life.