Alma from the First Encounter Assault Recon games is this toward Beckett to the point that she repeatedly attempts to rape him, and at the end of the game, finally succeeds. What makes this worse is that she cannot understand why Beckett fights her off.
Bloody Mary from Twisted Metal: Black. What's interesting is she doesn't have a specific love, but desperately wants a husband. And by desperate, I mean she stabbed her friend in the stomach on her friends wedding day, then put on her wedding dress and kept it on for two years, bloodstains and all. She's in the contest to get her dream husband, but when he tells her he'll never love her (despite being lobotomized by Calypso), she goes Ax-Crazy on him, then drives into the sunset to look for her Mr. Right, "even if she has to go through each and every man, one at a time".
Sapphire: Of course, I might've just gone back to slash you to pieces to vent my anger. You saved your own life. Heehee <3!
Occasionally, the fandom of Touhou portrays Alice as this, going beyond the usual Tsundere portrayal into seriously creepy territory. Highlights include attempting to put Marisa's soul into a doll to keep her forver.
Then there's Flandre, who loves to "play" with Marisa. And Meiling. And Remilia. And anyone else she "likes", really.
Koishi is this as well to a lesser extent, but more towards Satori and the character who defeats her in SA's Extra stage.
Yuka Kazami is often portrayed as Yandere for flowers.
Debatably the backstory for Parsee. The bridge princess youkai is the eternally-jealous spirit of a noblewoman who had a rather dire response to her husband's philandering, and was cursed into a demon for it.
Gil from Harvest Moon Animal Parade (Japanese version) seems like this when you get him to a certain heart level.
"I want to lock you up in my basement and keep you all to myself."
Gla DOS from Portal is an unusual case in that her primary goal is to chase Chell through a death maze and gets rather upset when she manages to escape. At the same time, she seems to have an unhealthy obsession with her captive.
Wheatley from Portal 2 might count, especially in the Final Battle. All his ranting is him being angry about Chell apparently choosing GLaDOS over him.
Yoshine herself has some slight tendencies, doing things such as putting a threatening note in the front seat of the taxi to make sure her Ryo sits with her in the back, strapping him down in the nurse's office and undressing him while he asks her to stop, and attempting to drug and kidnapped him near the end of her route.
Dark!Jaesa in the Sith Warrior class story in Star Wars: The Old Republic, if romanced, makes a hobby out of hunting down and murdering anyone the player character sleeps with.
Holiday in the Consular path will shock Tharan's bed until he breaks up with the Consular.
Persona 2 has Jun Kurosu. While it's not particularly touched upon in the main game, the drama CD turns him into an absolute psychopath over Tatsuya, to the point where even a friend having slightly better compatibility with him via horoscope is enough to send him into a meltdown. ...The creepy voice acting throughout the track (plus the humming and laughing) is enough to scare anyone for weeks.
Persona 3: Mitsuru has a particular Stalker with a Crush with overt Yandere tendencies. This girl stands outside the assembly room for the Student Council (of which Mitsuru is president) all day, is obsessed with everything Mitsuru does, threatens to kill you if you don't cough up swimsuit pictures of her after the Beach Episode, and innocently asks if members of the Student Council would be replaced if... something were to happen to one of them. Oh, and upon learning Mitsuru rides a motorcycle, she says she would be thrilled to be run over by those "burning wheels of LOVE!"
In Persona 4, there's an NPC outside the library who has a crush on an upperclassman. When she suspects that he has a girlfriend, she snaps at him and drives him away. Towards the end of the game, she places all the blame on the other girl and tries to kill her through indirect poisoning.
In Persona 4 Golden, the unseen upperclassman's gender is changed to female and the NPC now suspects that she has a boyfriend. The NPC herself however remains female...
Bioshock Infinite has the Songbird, whose sole purpose is to hunt down your partner Elizabeth and drag her back to imprisonment, out of programmed possessiveness. It's thirty-feet tall, and there's no way for you to kill it. Until you get to an ocean.
Mithos of Tales of Symphonia probably counts- his love for his sister Martel drove him to attempt to eradicate the entirety of the human, elven, and half-elven races by turning them into sterile, immortal, and emotionless zombies because his sister was killed because of Fantastic Racism. He snaps when Martel is briefly revived and tells him that this isn't what she wanted, and tells him her last wish is for him to stop it- he misinterprets it as she and he are Too Good for This Sinful Earth and both worlds should be flat-out destroyed. If anybody tries to tell him he's wrong, or says anything that could even be severely twisted around as being bad about his sister, he will kill you. Damn.
Dragon Quest VII has Kaya, a cheerful maid who's fallen in love with her rich employer's son, Iwan. Unfortunately, they're also caught up in a complex Love Dodecahedron... While Kaya initially comes off as the only one who isn't Wangsting and/or being an unhelpful Jerkass, instead working towards a solution, towards the end, she cracks a joke about poisoning everyone in town. While everyone is eating at a feast she prepared. Later on, you find out she wasn't joking about poisoning people, though she's narrowed her focus to a single target: her husband.
Jin Kisaragi from Blazblue is another male example, and dangerously skirt with Cute and Psycho. Any moment he's mentioned about his brother Ragna the Bloodedge, he drops all his cool exterior and goes Ho Yay to the max 'Oh brother...~' and expresses his 'love' by trying to kill him. Then there's the final boss Nu-13, who is usually robotic with everyone else, but if she meets Ragna, she also becomes a crazed lovestruck and tried to have him and when Ragna refused, she attempts to kill him. Then you realize that Nu is based on Ragna and Jin's sister. God, it sucks to be Ragna!
Sasha of inFAMOUS, the leader of the Reapers and the first Supervillain you fight is obsessed with Cole, whispering maniacal pleads for his love into his mind when he comes into contact with the sludge she controls. It might have something to do with the fact that she was Kessler's former lover and Cole is actually an Alternate Universe version of Kessler.
Why, Kessler? Why do you love her? I'll kill her, I swear it! I'll wear her skin like a robe!
Nuwangi in Utawarerumono. Sure, he is also an arrogant jerkass, but most of what he does is out of either desire for Eruruw or wanting to destroy Hakuoro. It's hinted from time to time that if the situation weren't what it was he wouldn't be as much of an ass. He's definitely not happy about what happens to Tuskuru.
In the Nancy Drew game Stay Tuned For Danger, the culprit is the rare male variety in the form of Dwayne Powers, whose motive for sending death threats to, and trying to kill, Rick Arlen comes directly from Rick dating the actress Dwayne is secretly in love with.
Depending on the ending you get, Maria/Mary in Silent Hill 2. It doesn't get much more Yandere than going One-Winged Angel and becoming the Final Boss because the target of your obsession rejects you.
James himself is most definitely overcome with love and more than a little unhinged.
Rachel, in the Sci-Fi Chapter of Live A Live. She snaps after Kirk, her boyfriend, dies and she carries his body to her room and acts as if he is sleeping. It's easily one of the creepiest scenes in that chapter, let alone the game itself.
In Pokémon Vietnamese Crystal, a very badly translated version of Pokemon Crystal Version, your rival seems to be a Yandere. Each of the player's encounters with him involves him berating the player, calling them things like "TRASHY" and "WEAK WORM", all while promising to beat them down. However, he also has a tendency to follow the player around and abruptly declare his love for them during his rants. It Makes Just as Much Sense in Context.
The StarCraft novel series The Dark Templar Saga suggests a similar relationship with the protoss being Yandere towards the xel'naga. After the xel'naga abandoned them, the tribes engaged in the biggest civil war the galaxy had ever known, killing each other because each held the others responsible for driving the xel'naga away. Many also hated the xel'naga for abandoning them... No surprise these became the Scary Dogmatic Aliens of the setting.
Mimmy is also this towards Henry, not allowing him to wake up so she can stay with him forever, even threatening to kill him when he suggests that they can live together in the real world. Since she is mostly a creation of Henry's mind, however, and technically not real, it is kind of obvious.
Lezard Valeth from Valkyrie Profile. When he first meet him, he kidnaps an elf girl who kill her and intertwine her genetic make-up with a human girl's to create a half-elf vessel for the main character, then uses his former teacher and her husband as bait by transforming the man into a monster and have him kill his wife. Then in the second game, he time travels and wreaks havoc with the timeline, kills so many people that it borders on genecide, and all just to get into Lenneth's panties.
No question, he's completely insane. But there's absolutely no point that he genuinely appears nice faking it during Silmeria doesn't count. Stalker with a Crush to the Nth degree, but Yandere could be considered a stretch.
Kingdom Hearts: Chain of Memories: Riku Replica goes absolutely apeshit if he thinks you'll get between him and Namine. Also, Marluxia's plan was to brainwash Sora into one of these for Namine, hereby turning him into a pawn to take over the Organization. It almost works, and after Sora and Riku Replica learn they were brainwashed, this doesn't affect their feelings much. (Namine ended up having to wipe Sora's memories of her to get him to recover.)
While many characters in Rule of Rose fit the bill, no one suits the trope better than Wendy, who kills Jennifer's dog Brown because she thinks that she likes him more than her, and when Jennifer reacts badly, she trains the neighborhood psycho to murder everybody.
A possible interpretation for Arvis of Velthomer, then Emperor Arvis of Grandbell from the Fire Emblem Jugdral games. Granted, he was already pretty fucked up from childhood due to being abandoned by his mother Cigyun when he was seven years old, but the scene towards the end of the first part in which he shows off his new wife Deirdre to her original husband Sigurd before pining the crime of high treason on him and burning him to death with his Falaflame magical tome is pretty easy to interpretate as him being Yandere for her.
In the second part of the game we have Prince Julius of Velthomer who happens to be Arvis and Deirdre's son. The only person he shows affection to is his girlfriend, the local Dark Magical Girl Ishtar, and when he finds out that her bodyguard Reinhardt seems to be a liiiiiiittle too close to her for his comfort, Julius forces Ishtar to fire him under the threat of killing him the next time he sees them together. To be fair, Julius has been the Soul Jar for the evil god Lopto for a while already when that happens, therefore we don't know if he's a Yandere per se or because of Lopto.
Tharja from Fire Emblem Awakening epitomizes this. She follows the Avatar around everywhere (regardless of the Avatar's gender), counts how many times s/he turns over in their sleep and how many slices of fruit they peel, and has a lock of their hair in her bag, among others. You can also have the Avatar (if male) marry her if you so wish, which gets you this line from her Confession scene:
Tharja: I can't believe you made me love you! ...Course, if you back out, I'll murder you in your sleep.
Bowser from the Super Mario Bros. series games is actually this to Peach, which explains why he always kidnaps her in the first place.
Both Catherine and Katherine are both in love with Vincent, and Catherine outright states that she'll kill him or any girl.
Planescape: Torment has one in Ravel Puzzlewell, who refuses to let her love leave her a second time when he comes to visit...
Ravel Puzzlewell: "I shall NOT let you leave — I have the power to KEEP you here, and I shall USE it. My black-barbed maze shall NOT allow you to travel beyond it while I LIVE, my precious, precious man..."
Another male example is Anton Herzen from Professor Layton and the Diabolical Box. He waited years in a mansion for the return of his fiancée and when he finally sees someone who looks exactly like her (for good reason), he goes completely mad and tries to kill Layton because he thinks his long-awaited fiancée has been cheating on him. He got better, thankfully.
Camos O. Laphroaig of the Hell Hounds in Galaxy Angel is a Yandere toward Milfeulle, he always calls her honey and somehow hopes his actions (including trying to shoot her down) will win her over. He finally croses over to true Yandere territory when he's taken over by the black moon.
In Tales of the Abyss, Dist the Reaper is in the aftermath stage of this trope. As a child, he was clingy and obsessive over Jade, always wanting to remain at his side - when Jade finally rejected him once and for all, he became the raging, narcissistic person we see in the game, now obsessed with taking revenge on Jade instead.
Tales of Legendia has a tragic example with Shirley, who for so long is actualyl a Love Martyr trying NOT to be a Yandere, and even after Senel rejects her love and she becomes Brainwashed and Crazy, she tries to hold on. But then Manipulative Bastard Maurits reveals a devastating truth about Senel that finally causes Shirley to snap and give into Nerifes' full control as means of revenge against Senel. She gets better, fortunately, when Senel apologizes and frees her from Nerifes later.
The Boss from Saints Row: The Third can be one to Pierce, if you choose the Eastern European Female voice set. While probably not the jealous type (No one else is ever seen making a pass at Pierce, so it can't be said of whether or not she actually is) she frequently makes it clear that she has a thing for him, ranging from wondering if she can get cameras installed in his room, considering sending him a sex machine from "a secret admirer," offering to be his dominatrix, and finally admitting to wanting to make love to him in front of a live studio audience. If this doesn't seem crazy enough, this is the same woman who drove a tank out of the back of a crashing plane, parachuted into a penthouse party and immediately proceeded to kill everyone in sight, and has a murder record on her that runs into the thousands. In Pierce's position, it would most likely not be a good idea to even kindly ask his...admirer to back off.
One sidequest from The Godfather 2 involves the questgiver asking Dominic to help snap his Yandere girlfriend out of it by force.
Alois Racini from Amnesia: The Dark Descent expansion Justine, he is one of the suitors who after getting tortured and blinded by "beautiful" Justine keeps creeping around looking for her, wanting to kill her and keep her dead body with him forever.
Mia Touma in her route of Duel Savior Destiny goes absolutely off the deep end starting with raping someone with drugs, attempting to petrify an ally, leaving that ally to die and finally outright switching sides to an Omnicidal Maniac faction out of jealousy.
In Ib, Mary is obsessed with forming a friendship with Ib, displaying jealousy towards Garry and trying to ditch him a couple times, even at a point where it's clear he's in trouble and needs help. She tries to attack Ib when she thinks Ib will leave her. She chases after Ib and Garry with a palette knife. When she catches up to them she locks them in her toy box. If you anger her enough over the course of the game, she murders Garry. And in the ending "Welcome to the World of Guertena", Ib collapses in despair at seeing Garry go incurably insane and Mary decides the best solution is to keep Ib and Garry trapped in her world forever.
Then there's Mary. Once Garry finds out what she really is, she becomes very possessive of Ib and gets upset if she thinks Ib is going to leave her. She even goes out of her way to kill Garry in order to be Ib's sister in one ending.
The RED Soldier from Team Fortress 2, who used to be the former roommate of the luckless magician Merasmus. After being thrown out of Meramus' apartment for being a lazy bum, trashing Merasmus' castle and getting the magician ejected from said castle by the authorities, and burning Merasmus' physical body after the angry magician transformed into a ghost form to attack the teams of mercenaries, the obsessive relationship turns into creepy homicidal stalker territory in "Ring of Fired", the first issue of Valve's latest six-part TF2 comic, when Soldier casually wanders into Merasmus' new apartment and snaps the neck of Tom Jones, the new roommate.
Soldier: "The heart makes its own rules, Merasmus."