Tokiwa spends the first eight episodes like this for Meirin, going so far as to set their school on fire in order to threaten her. It's later subverted, though, since he was possessed by an evil spirit that wanted to kiss her in order to possess her.
In Samurai Harem: Asu no Yoichi, the only reason Ukyō Saginomiya wants to kill Yoichi is that the latter "came between" him and his childhood crush, whom he's basically stalked for several years.
Germany keeps a diary of observation on Italy. It makes some sense, as Germany is attempting to train him. But if Germany really is a grown-up Holy Roman Empire, then it just makes it seem like he hasn't grown up all that much.
France is sometimes shown to have these tendencies. He was once shown sneaking up to Austria's house, watching him without his knowledge while he was playing the piano, and commenting on how attractive he finds him.
Suruga from Bakemonogatari is dangerously in love with Hitagi. So much so that she starts stalking Koyomi after he hooks up with Hitagi and tries to beat him to death one night.
Reimi from Bamboo Blade has made a habit of stalking Miyako "Miyamiya" Miyazaki when she learned that Miyamiya beat up a boy who she had a crush on in middle school.
Battle Royale: Sho Tsukioka is effeminate in manner but humorously masculine in appearance and uses his skills as a Stalker with a Crush to tail Kiriyama. He's also a borderline alcoholic drag queen with an irrational crush on Kiriyama and overall thinks like a total lunatic.
Beauty Pop: Kazuhiko Ochiai when he develops a crush on Kiri. He chases after her, is shown secretly watching her from behind without her knowledge, and even has Kiri's picture as his cell phone's wallpaper. In the end, although Narumi and Kiri have married, he still refuses to give up on her, even teaching Kiri and Narumi's kids to call him "daddy". He also often schedules appointments after hours for Narumi to prevent him from going home to Kiri so that Ochiai can gladly go in his place.
Creed Diskenth takes this to a creepy extreme. He murdered Train's only friend because he thought she had cast a spell on him, stalks Train and constantly threatens people he loves in the belief that Train will join up with him. In the anime, his stalker-ish tendencies go to the point where he uses his subordinate's spy insects to watch Train sleep. It's not exactly clear in the manga just how much of this is sexual, but it's pretty clear in the anime when he's daydreaming about Train while stark naked in a rose bath.
Kiyone and Sentarou follow Ukitake everywhere he goes, especially when he doesn't want them to. Kiyone is in love with him, so for her it's particularly zealous.
Soifon's obsession with Yoruichi is Played for Laughs. In one omake, she stalks Yoruichi in a desperate attempt to see her naked. She even helps Kiyone obtain pictures of a stripped down Ukitake in exchange for Kiyone's help capturing pictures of a naked Yoruichi. They capture the unassumingly friendly Ukitake off-guard, but Ukitake manages to warn Yoruichi who gains revenge for both of them.
Keigo's sister Mizuho has a fetish for men with bald heads so falls for Ikkaku the moment she meets him. In the anime, she stalks him everywhere.
Solomon spends most of the series as one of these. After Saya gently rejects him though, he backs off and decides he'll still love and protect her without attempting to force her to love him back. Then he accidentally gets killed by her bloody sword trying to protect her from James.
Karl also had this for Saya, he wanted to kill her while she kills him.
Diva had also developed this kind of obsession with Riku after she met him; sadly, it turned into the other kind of stalking...
Tomoyo from Cardcaptor Sakura directed towards Sakura. Much less aggressive than the average stalker, however she does make her wear several interesting outfits throughout the series, films her wearing them, and watches the aforementioned recordings alone repeatedly...
Mao is C.C.'s stalker with a crush. Seriously, he listens to a recording of her voice comforting him in his headphones constantly, although part of this is to prevent himself from being overwhelmed by hearing everyone's thoughts with his out-of-controlGeass.
Volume 6 of Confidential Confessions deals with one of these. None of it is played for laughs. The stalker is legitimately creepy and the protagonist is genuinely terrified of what he might do.
In Darker Than Black there are a few stalkers with a crush. Maki has an obsessive affection for Amber and tries to kill Hei because of this and likely would have tried the same against Amber's other followers. Also, Kiko, who has a crush on Hei, gets angry when her friend Mayu also starts after him, saying, "Only I can stalk him!" And when we first see Kirihara in the second season, she was watching Hei's star through a telescope, which is probably the closest it's possible to get to stalking him when he's not intentionally staying in one place. Lampshaded when her friend at the astronomy department suggests that she really needs to get over him and find another guy. And yes, Hei has a lot of stalkers.
The second season has Norio, who has a rather creepy stalker-crush on Suou. This is made significantly worse by the fact that they're portraying him as a Dogged Nice Guy.
In a flashback in Death Note, Misa Amane encounters one and, after she refuses his confession of love, he plans to kill her and then himself. This would have ended with her death, but Gelus the shinigami writes the killer's name in the Death Note to prevent him from killing her, and dies for violating one of the shinigamis' laws against saving human life. Misa eventually (ironically) becomes a Stalker with a Crush toward Kira, admiring him for killing the burglar who killed her parents and forcing Sakura TV to make a broadcast while pretending to be Kira in order to lure him out.
The evil and brilliant scientist/surgeon/sorcerer Dr. Muraki in Descendants of Darkness lust for and stalks the shinigami Tsuzuki. Before that, he raped Hisoka and placed a curse that caused Hisoka's death. And while the second one was just because the poor boy saw way too much, the first one is a bit more complicated: Muraki wants to revive his dead brother Saki using Tsuzuki's body. So he could kill Saki with his own hands.
Nanami in Digimon Savers. She had a crush on Touma, although it seemed like she could have been seducing him just to betray him afterwards if he said "yes".
Dirty Pair Flash episode "Barairo no Bish?nen [My Boy]" featured a young rich boy obsessed with Yuri (no, not that"Yuri"). He had observed her from a distance, and built a robot based on what he believed her to be like (which was very different than she actually was). Yuri tried to convince him to stop believing in his false impressions of what she was like. She hoped that by doing this, he would then fall in love with the real Yuri. Unfortunately for Yuri, this just ended his crush on her... at which point he began a relationship with a girl who had been a Stalker with a Crush for him. Yuri was not happy about this result.
Daisuke Hagiwara from Dragon Drive is like this towards Maiko Yukino. In the anime, he always refers to her as "My sweet honey" (in Gratuitous English in the Japanese version). The odd thing is how he evolves from an antagonist to being a practically sympathetic character and a member of the series' ¡Three Amigos!, despite staying an unsavory Smug Snake the entire time. Also bizarrely, he gets along rather well with main character Reiji Oozora. Well, at least when they don't think about who they're palling around with... The fact of the matter is that they're simply Not So Different.
Gauron from Full Metal Panic! towards Sousuke. Especially obvious in TSR, where he orders the destruction of a huge city to lure Sousuke there, spreads an incredibly complicated and cryptic message that no one in the world except Sousuke would ever understand, orders the two beautiful girls who adore him to go to their deaths just so that he can Murder the Hypotenuse — all for the sake of his obsessive and sick love for Sousuke. He also apparently knows a lot of information about Sousuke's background and history that he shouldn't even know (considering that no one else in the series, including Kalinin, knows some of that stuff), making it very likely that he researched and stalked Sousuke even more than what was shown. Something worth noting is that, as shown in the novels, he was actually recording and watching footage of Sousuke without Sousuke even knowing. Gauron's partner is shown to be disgusted and annoyed by Gauron's euphoria and ecstasy at watching "his precious boy." It's almost as squicky as it sounds.
Considering he's apparently had a thing for Sousuke since the kid was twelve (Gauron? Probably at least forty), it's probably even worse than it sounds.
Leonardo Testarossa became one of these for Kaname. That being said, he's much tamer (and saner) than ol' Gauron up there. But then again, he once forced a kiss on Kaname, kidnapped her after besting Sousuke (in a gentlemen's duel), and personally assured him that despite his attraction to her, he wouldn't force anything, and will see to that nothing untoward should happen. Later on, however, he becomes so enraged with Kaname not giving in to him, and sort of "betraying" him by finally declaring to Sousuke that she loves him, that he slaps her hard enough to make her fall to the ground, speaks to her very rudely, and generally tortures her (more mentally than physically) in order to weaken her mind so that she won't be able to resist his plans of world-domination.
Yuno Gasai. Obsessively in love with the protagonist Yukiteru Amano, to the point where she follows him around all day, breaks into his house, sends him hundreds of emails over the course of an hour, doesn't think twice about using sharp weapons to kill those that threaten his life or their relationship and at one point goes so far as to drug him, kidnap him, and lock him in a room chained to a chair so she can be with him and protect him. However, Yukiteru willingly teams up with Yuno (even if he doesn't really love her) to help both their chances of survival against people that are truly insane. Of important note about Yuno is that while she is actually the Goddess of yanderes, there are actually three different Yunos from three different worlds, only the first of which truly fits that category. This is the one we see doing all of the horrible things we see. The other two are more in line with this, as they are far more normal people and are never shown performing any serious acts of violence on-screen. The reason the first seems to be so insane and violent is because she's already been through the survival game once before and cruelty and murder are no longer a big deal to her.
Akise Aru becomes one of these towards Yukiteru shortly after meeting him basically. He's shown to be immensely interested in him, and follows him around, sticking his nose into Yukiteru's business. He even performs a Forceful Kiss on him...right in front of Yuno.
This seems to be the standard adversary for a bodyguard in Game×Rush; Memori gets a lot of jobs where he must protect his female clients from Stalkers with Crushes, only to have said clients becomes Memori's stalkers in turn. Also played with when, early on, Memori accuses Yuuki of being his stalker; later, Yuuki wanders to Memori's house without thinking about it and wonders if he really is a stalker. Considering how Yuuki shadowed Memori since they first met, the question of whether he's Memori's stalker might be moot.
Utsumi from GE - Good Ending was content with being just this until he was caught by Yuki.
Get Backers has Takuma Fudou towards Ban Midou. He follows Ban everywhere, constantly screaming at Ban to "give him his body" and "meet his throbbing desires." Ban even lampshades it with annoyance, calling Fudou a "damn stalker zombie" - which Fudou seemed very happy to be called. Fudou is definitely an interesting example of an Ax-CrazyStalker with a Crush - he's so obsessed with Ban, he even readily admits that he gets put off and upset when Ban ignores or doesn't notice him, and that he wants Ban's eyes to only be on him. He tried to violently kill Ginji, telling Ginji he never liked him because Ban doesn't even notice his existence when Ginji is around - and that this will all be fixed when Ginji is out of the way.
The woman (and spurned lover) who was stalking Paz in one episode of Ghost in the Shell: Stand Alone Complex: 2nd Gig. She went so far as to get her brain transplanted into a cyberbody that looked exactly like Paz's cyberbody. They ended up in a knife fight to the death... and there's no way to be sure it was the real Paz who won. Truly, Hell Hath No Fury...
In Ghost Talkers Daydream, Mitsuru is so obsessed with stalking Misaki, that he's repeatedly broken into her apartment and stolen entire drawers of her underwear. Though he leaves money for her to buy new ones that he intends to steal later, after she's worn them. Worse, he's gone so far as to bug her apartment and even has recordings of her using the toilet. Misaki has even threatened to call the police if he doesn't stop... which he eventually does, because of Ai.
Kondou, played entirely for laughs. Especially when Otae, the woman he's stalking, begins to beat him in increasingly violent ways. Also, Ayame as well.
Even more hilarious is that unlike Kondou (who just does not know when to quit), Ayame "Sa-chan" Sarutobi actually enjoys being abused/rejected by the object of her affection Gintoki.
Girl Got Game: Akari Tojo, the team manager is this towards Kyo, with some Yandere tendencies thrown in for good measure.
Girls Bravo has a few. Lisa became one towards Yukinari after finding that his appearance matched a description in her horoscope for her soul mate, Kosame became one towards Kirie shortly after fighting her, Hijiri was obsessed with Miharu since they were both children but after being defeated by Kirie she forgot about Miharu and started obsessing over Kirie instead, Fukuyama is pretty much one towards any pretty girl that takes his fancy though his most frequent targets are Kirie and Koyomi, and Yukina becomes one towards Yukinari after being shown kindness by him.
Shuichi from Gravitation chases Yuki constantly, despite being rejected, verbally abused, and often being called a little brat. They eventually end up together.
Teshigawara in Great Teacher Onizuka. However "stalker" and "crush" are understatements of what this guy feels for Azusa Fuyutsuki.
Goldie, a mob leader who has a habit of using the drugs her organization produces and sells to make people who catch her eye into mindless slaves devoted to her pleasure. When Rally manages to resist her and escape, their relationship quickly turns into this, to the point that Goldie allows herself to be arrested and then jumps bail specifically to draw out Rally in a personal challenge.
Before Goldie there was Gray, who falls madly (emphasis on the mad) in love with Rally after she blew off his hand. He claims he wants to return the favor with interest by amputating her arms and legs, but he also tells her that he loves her. Try to scrub that image out of your brain.
Urushizake from Haru wo Daiteita, a member of the paparazzi who styles his hair and dress to look like Katou's lover Iwaki-san, has an apartment within binocular-watching distance, and ultimately uses his influence in the media to assist Katou on one of his sets.
Hayate the Combat Butler: While Athena watching Hayate from afar is more like schoolgirl pining, Chapter 304 reveals that Kotetsu has become this when he follows Hayate into the public bath and directly states this as the reason why he is there and states that he loves Hayate.
Higurashi: When They Cry - Rena is a stalker in Onikakushi-hen, the first arc in the series. However, it is later shown she merely was afraid for Keiichi's safety, since he was often left alone due to his parents having to leave town and because of his similarities to Satoshi. She didn't want him to get "Demoned Away" like Satoshi supposedly was. Rena is also often hinted to be in love with Keiichi.
Honoo No Alpen Rose: Count Germont, who wants to have Jeudi because she looks a LOT like a woman he loved in the past.
Hunter × Hunter: Hisoka obsessively stalks Gon because he wants to kill him in a battle when he becomes strong enough for his liking.
Torako from Hyakko keeps following Touma around and tries to be friends with her, even though Touma is clearly not interested. When asked whether she is obsessed with Touma, Torako simply answers that she indeed is. Sure, her behavior is not as egregious as most of the other examples, but she is at times close to crossing the border of what is acceptable.
The "Strange Lolita" in Ibitsu goes from victim to victim, stalking them and insinuating herself into their lives, though she seems to be seeking more of a (albeit extremely twisted) brother-sister relationship than a romantic one.
Naraku's entire initial reason for becoming the villain in the first place was a desperate desire to get into Kikyou's hakama and punish Inu-Yasha for being her boyfriend. Wanting to be with Kikyou remains a driving desire of his right until the end.
Jakotsu becomes obsessed with Inuyasha from the very first moment they meet. There's a Running Gag in the story that people find Inuyasha's ears so cute they have to touch them. Jakotsu twists this. He loves Inuyasha's ears so much he wants carve them off and keep them for trophies. After he's had his way with Inuyasha, of course.
Once Kouga decides to make Kagome his, he follows the group everywhere trying to convince Kagome to choose him over Inuyasha.
In anime filler, when Sesshoumaru retreats in agony after losing his arm to Inuyasha, he destroys an army that's in his way, accidentally saving the life of Princess Sara and her family. Convinced he personally saved her, Sara regularly sneaks into the forest to spy on him while he's recovering. When she overhears what happened, her obsession convinces her to voluntarily become possessed by youkai to gain the power to kill Inuyasha, steal Tessaiga and present Tessaiga to Sesshoumaru as a gift of her desire. Sesshoumaru's even less impressed by all this than Inuyasha.
Narciso Anasui's ideas for courting Jolyne leave something to be desired. For example, trying to get F.F. to push Jolyne down a flight of stairs, just so he can catch her, and trigger her love for her savior.
Yukako Yamagishi towards Koichi. Although after he successfully defeats her, she greatly tones down her aggression.
Joushuu Higashikata, almost underlying into the whole Yandere territory, towards Yasuho Hirose. Sure, he is incredibly idiot enough to not understand that Yasuho doesn't want to do anything with him, but is still conflicted with Josuke being in between (his family, mostly...), and of course, he thinks Yasuho is still in love with him... giving unfortunate results in the process.
The former student body president, Megumi Sokabe, from K-On! towards Mio. A strange example in that she is not in love with Mio, nor is she even a lesbian. She just finds Mio and her antics extremely adorable, and even ended up literally stalking her through the school a few days before graduating out of sadness that she would no longer be able to see her.
It's worth noting that she's not the only one who has a thing for Mio. Even at an all-girls school, Mio manages to have her very own fan club, with real members, membership cards, and everything. In fact, Megumi also doubles as the president of the Mio Fan Club.
Kaguya Hime: Mayu doesn't start off as a stalker, having the advantage of being Akira's adopted sister, but when they're separated, she will do anything to find Akira. Julian is this to Miller to some degree (but an ultimately really nice one).
Kare Kano: Arima's dark side. Any time that he comes onto the screen, you just know Arima is seconds away from shattering. This is made worse because to the outside world, he appears to be a put together, genius with his only match being Yukino, his girlfriend. It's scary to slowly see his thoughts morph from wanting to be with Yukino, to wanting to isolate her from everyone and keep her just for himself. His fighting with these thoughts proves that Arima is a good guy, but him imagining tying Yukino in chains does not bode well for their relationship. This is a rare case of Stalker with a Crush in which not only is the stalker in a committed relationship with his crush, but he is also portrayed as so sympathetic that you just want to save him from himself.
Gokudera is a much nicer and saner version of a Stalker with a Crush towards Tsuna. He's constantly following Tsuna around and surprising him by showing up where Tsuna doesn't expect him. Also, in chapter 292 Enma leaves Tsuna's house in the middle of the night only to be immediately encountered by Gokudera approaching the house with a flashlight. Gokudera wonders why Enma is not guarding Tsuna and Enma replies that he left his school supplies at the guest house and leaves. Gokudera expresses annoyance at this and proudly states to himself "I knew it. The only one who can manage to guard the Tenth 24/7 is me!!!" He becomes unreasonably jealous of anyone who is close to Tsuna, and is even shown watching Tsuna and getting incredibly pissed at Yamamoto for being so friendly with him. Not to mention his violent reaction when Chrome kisses Tsuna.
Haru could be considered one at her very first appearances, from when she liked Reborn.
Rune in Karakuridouji Ultimo is one to Yamato, the main character. Hell, he even has this huge framed painting of Yamato in his room. These feelings later give him a reason to go over The Dark Side, and do very terrible things to Yamato.
Kiryu Setsuna from Kengan Asura is obsessed with the main character Tokita Ohma, and appears sexually aroused at the mere thought of killing him in a fight. He stalks Ohma throughout the tournament, and displays Yandere tendencies towards him as well.
Koharu, the eponymous character from Koharu No Hibi, certainly is one of these, as she constantly follows the main character, Akira, around. She later becomes his girlfriend, not that her behavior changes any.
Evangeline was one of these to Negi's father. She followed him around in a shapeshifted/illusory form of herself as an adult but he knew she had the body of a little girl and said he didn't like brats, plus he was already Happily Married. Then he trapped her in a magical barrier to keep her from following him around everywhere. Before anyone asks, she looked no older than than she does now.
Tomoe from Mai-Otome, who had a crush on then-Coral Otome Shizuru, and once snuck on campus to get a glimpse of her. By the time Tomoe's old enough to enter Garderobe herself, it soon becomes apparent that those tendencies have not diminished with age.
Kei's rather possessive of Miki, as she's one of his very few friends and he does some serious work towards isolating her from Yuu. Anime only characters Michael and Jenny arguably qualify, as well as anime!Suzu. Satoshi is a more gentle version of this trope in regards to Meiko.
Märchen Awakens Romance: The Phantom towards Alviss. Also, Chaton on Alan and it’s played for laughs. Technically Dorothy is this to Ginta as well.
Masako Natsume is also a serious case to the point of erasing all memories of Kanba from his ex-girlfriends' minds. It laters turns out it's not as simple: Kanba is her older twin brother, they were separated as children (with Kanba being first kicked out of the Natsume clan alongside their dad and then living in the Takakura home, while Masako and their little brother Mario are stuck with their abusive grandfather), and she desperately wants him to come back home.
Though it's speculated that Glemy actually is Gihren's bastard son who convinced himself that he was a clone of Gihren to cope with his Parental Abandonment; in said case, Roux would be stalked by the child of Adolf Hitler's stand-in. It still sucks.
In Momokuri, main character Kurihara Yuki is obsessed with her schoolmate Momotsuki Shinya (aka Momo-kun), whom she finds adorable. She follows him wherever he goes, gathers information about his schedule to increase chance meetings, and takes secret photos all the time. When she got her hundredth candid shot she finally confessed and started going out with him, but this didn't curb her tendencies at all. Instead, it made it easier to get information and arrange chance meetings, and also made it possible for her to obtain and preserve his used straws, leftovers, bits of sand from his shoes, and just about anything else that has touched him that she can fit in a vacuum-packed bag. All of this is Played for Laughs because she really doesn't meant Momo any harm; it's just that she really, really loves Momo, but is too shy to be more forward with him when they're actually together.
Eva in Monster. Getting revenge on Tenma for leaving and rejecting her is probably the only thing keeping her from offing herself, really. It becomes more pathetic when you realize that she was the one who dumped him first. Sometimes, she will go out of her way to intercept Tenma's dates and scare them off.
Mother Keeper: Syal had a stalker as a master, Alan, when she was a human slave. This ended badly: she became a slave to earn protection for her adopted family and her sister/mother/lover... whoever that woman was. Then Alan gets so enamoured with her killing spree that he blatantly executes her adopted family to get the sister/ figure and have them fight each other, which breaches the slave trader's contract of protection, who then retalliates by tipping off Eden soldiers about the illegal deathmatch ring that Alan is a part of, who kill Alan, the sister/ figure, and as an insult to injury, when Syal is pleading for someone to save her sister, the sister dies and Syal is turned into an unstable immortal instead.
Downplayed with Hinata. She has a crush on the titular character because of his ambition and ideals, but suffers from painful shyness, and is thus forced to admire him from afar. Also, she doesn't follow him around and her feelings are genuine, rather than an overobsessive crush. Her feelings become a symbol of real love when she attempts to save his life from Pain, although by that point, she had already dropped this behavior entirely.
Played straight with Karin. She is massively attracted to Sasuke after he rescued her during the Chunin Exams, but this takes a sharp turn when Sasuke sacrifices her to kill Danzo. She later forgives him for this anyway.
Nightwalker: Cain wants to have a good relationship with Shido, that's all! Of course, his idea of a good relationship revolves around them terrorizing the night together... And his methods involve destroying things that Shido holds dear until he gets the picture.
Tokigawa Takaai in Okane Ga Nai is one of the creepiest examples of this. His Ayase obsession knows no limits: Not only does he have a room filled with pictures of him taken without his permission as he actually collects items that Ayase has discarded such as water bottles and has been doing so since High School, having deliberately flunked a year so that he could enter University at the same time as Ayase. Apart from all this, he comes up with an elaborate scheme to force Ayase into a relationship that includes bugging his room and eventually tying him up and threatening him with a knife in what can only be qualified as Attempted Rape.
Lady Alvida from One Piece. She joined Buggy in order to find Luffy in order to "make him her man". Since he was the first person to ever hit her, this may have some sadomasochistic undertones.
Abasalom maybe be the creepiest Villain in One Piece having "Devil fruit" power invisibility, Absalom spies on the beautiful pirate Nami (Main female character) while she is bathing and holding her against a wall decides she is "fit" to be his bride, he then stalks her relentlessly though the majority of the arc and succeeds in abducting her and trying to marry her against her will in a And Now You Must Marry Me fashion. Nami is then rescued by fellow pirate Sanji who follows the Always Save the Girl trope and fights Absalom for his perverted and creepy actions towards her in a No Holds Barredbeatdown.
In the latest chapters, we have Decken towards Princess Shirahoshi, to the point her Overprotective Dad has to keep her locked up for ten years to keep her safe from the guy. Then again, he "sends" love letters to her in the form of swords and broadaxes after she rejected his marriage proposal and he firmly believes that her fate is either marry him or be killed by him.
A strange example, because the reason he wants to marry her is to use her as a weapon.
Oniichan No Koto Nanka Zenzen Suki Ja Nai N Dakara Ne: Poor Shuusuke. The two girls that have the hots for him are both this. Nao knows when he learned to collect pornography, read it and hide it. As for Iroha... let us stop with her knowledge on how often does he masturbate and which hand does he use for that, OK?
Oniisama e...: Miya-sama. Somewhat unusually for this trope, it's not Henmi, the object of her affections, that is the target of her stalker behavior, but Nanako, his pen pal who Miya-sama believes he is romantically involved with. Also, the room at her summer house is full of creepy dolls and obsessively arranged items of memorabilia from the day she first met her crush Henmi, which she has since kept completely unchanged for six years and forbids anyone else to enter.
Harry MacDougall to Melfina in Outlaw Star, including a symbolic attempted rape sequence. Hitorige of the Antem 7 was so obsessed with Suzuka that he had plastic surgery to make him look like her.
In Peacemaker Kurogane (especially in the manga), Suzu becomes obsessed with Tetsunosuke, constantly having his every action monitored. He becomes jealous and scared when Ryoma decides to take Tetsunosuke away with him, taking drastic action to kill Ryoma and frame it on Tetsunosuke so Tetsunosuke won't be able to get away from him. This results in much Foe Yay.
Me-Mania in Perfect Blue is one for Mima of CHAM, and doesn't take it well at all when she leaves the group to start an acting career, going from sending her threatening e-mails to murdering people around her to eventually trying to rape and kill her.
Phantom Quest Corp.subverts the trope in the first Incident File ("Kiss of Fire"), which has Bosco tailing Makiko whenever she goes out at night. While he is in love with her, it's revealed that he was protecting her from another vampire, who had recently reincarnated and was repeatedly victimizing her.
The initial basis of HeatTagShipping (Dawn/Conway) in Pokémon. Helped by the fact that Conway grows considerably less creepy in future appearances. Well, kind of...
A mini-comic in one of Toshihiro Ono's graphic novels plays with this trope by having a Ditto impersonate Ash and do naughty things to Misty (touching her butt and watching her shower), causing her to take vengeance on the real Ash.
Meanwhile, in three straight movies in a row, Brock has a little blue book containing very accurate information on famous female celebrities that he and the gang just happens to come across...
Late in Pretty Face, Dr. Manabe picks up one of these. He manages to discourage her by using the protagonist to convince the stalker that he wasn't interested in women.
Parodied a bit, since one would think Yuuji Hitouji and Koharu Konjiki from Shitenhouji are just playing up the gay act as a part of their playing strategy, but sometimes Yuuji seems to take it a bit beyond that...
In the het side, sometimes Tomoka Osakada seems like one of these too thanks to her occasional but very obvious jealousy towards other girls who fangirl Ryoma (with the exception of Sakuno, that is). Again, played as a running gag since it's a side-effect of Tomoka being just a twelve year old.
While the list of who is obsessed with who is quite complex, only a relatively few people exhibit actual stalker tendencies... though just about everyone exhibits Mad Love.
Ryoga pretends to be Akane's pet piglet so he has an excuse to be in her presence as much as possible and get to hear her innermost secrets.
Mousse has been begging Shampoo to be his girlfriend since they were three and, despite her often violent constant refusal, even followed her to Japan to not only continue doing so, but also to try and murder the guy she's actually interested in.
Gosunkugi exhibits classic stalker behavior, especially in the manga.
Tatewaki Kuno frequently pops up out of nowhere to try and hug/grope Akane or Ranma-chan — ironically, his sister, who is the crazier of the two in terms of actual romantic ideas, stalks Ranma the least of the siblings.
A ridiculous number of Sailor Moon villains. Queen Beryl (Mamoru), The '90sanime's Ali and Ann (Usagi and Mamoru respectively), Prince Demand (Usagi), Chibi Usa as Black Lady (Mamoru, in the manga), Fish Eye (Mamoru), Nehellenia (Mamoru, anime only), Galaxia (Mamoru, manga only), and Fiore (Mamoru, R movie). So basically, almost all of them are going after the heroine's lover.
It is heavily implied in episode 106, "The Distant Days of Uranus," that Michiru was one of these to Haruka going way back before she even knew that Haruka was destined to become Sailor Uranus.
Saiyuki has two: Chin Yisou, who is fixated on Hakkai, and Go Dougan from the Requiem movie, who goes to ridiculous lengths to get Sanzo's attention. Both of them are really blatant about it, too - half of Yisou's I-dislike-you dialogue with Hakkai sounds like foreplay gone wrong, and Dougan... oh, Dougan appears to be giving head to a shikigami replica of Sanzo at one point...making him perhaps the largest uke in the series. IT'S A SHIKIGAMI AND STILL HE 'BOTTOMS' TO IT?
It's mentioned several times in Sakura Gari that anyone who starts having a relationship with Souma ends up becoming his stalker. Souma, in turn, starts acting this way towards Masataka. And Sakurako, Souma's sister, acts this way towards him.
3-gatsu no Lion's Kyoko Kouda is in love with Gotou. However, Gotou openly referring to Kyoko as a stalker despite being acquainted, even if half-jokingly, indicates that their relationship is not reciprocal, and she just shows up wherever he is without necessarily getting his approval. Apparently, he just allows her to follow him around for unknown reasons.
Matoi's entire characterization in Sayonara, Zetsubou-Sensei is the completely unsubtle stalker who follows Itoshiki-sensei around everywhere, wears the same clothes as him, and resides either under his desk or in his house because of her "deep love" for him. She also did it to all of her crushes before him. Also, her name literally means "to stalk". Not to mention following him into the men's bathroom and standing directly behind him watching while he's using the toilet. Plus, in her room she has a wall covered with pictures of him and has admitted to having read through Nozomu's mail and disposing of them before he gets a chance to read them.
This is apparently normal of her, as her mother nonchalantly asks that she now has a new obsession/target of affection.
Also parodied with the Chain of Stalkers. Matoi has someone stalking her, and there's someone stalking that person, and someone stalking that person, and so on.
As indicated by the page picture (of Kaere/Kaede), Matoi is far from the only example in the cast- just the most extreme.
Onodera Ritsu from Sekai-ichi Hatsukoi was like this to Takano Masamune when they were in high school together. Onodera was fully aware of how creepy and obsessive his actions were but lacked the courage to speak to Takano for a long time. He even went through the trouble of tracking down the books that Takano read but wrote a fake last name to partially hide his identity.
Mikogami Hayato from Sekirei combines this with Gotta Catch 'Em All, becoming fixated on particular Sekirei he wants to add to his collection.
Sgt. Frog: Momoka. She has her bodyguards spy on Fuyuki to find out what kind of underpants he wears. And that's only a minute fraction of the stuff she's done.
Better(?), Chiruyo Tsukigami, seeing as how she spies on Fuyuki personally, snapping pictures on her camera phone and scribbling in her notebook to boot.
Shimoneta plays it for laughs, fanservice, and drama, depending on any scene with Anna. Public Moral Decency laws in Japan have legally prohibited all pornographic material and anything that can be remotely perceived as such (including basic Sex-Ed), for the last 16 years. Which combined with Anna's sheltered upbringing, has left her sexually repressed with no understanding of what is, or isn't, proper sexual conduct. So when Tanukichi accidentally kisses her, it awakens her body's pent-up urges; causing her to develop an unhealthy obsession with him. To such an extreme that she can literally track him by the scent of his boxers!
Reino from Skip Beat! towards Kyouko. Initially to steal her away from Shou and anger him; nowdays, he just fell in love with her dark and hateful side.
Soul Eater has a bit of an odd example: Soul has his fan club full of girls requesting to become his partner. Very few members of this Unwanted Harem are ever seen, although around Chapter 69 of the manga, a girl with huge eyes starts following both Maka and Soul everywhere, peeking at them from behind every corner. Soul seems completely oblivious about it all, handwaving his request letters and attributing them to his becoming a Death Scythe (and Maka's lack of letters due to her lack of sex appeal), but he has yet to see his stalker. Maka, on the other hand, has been confronted and has had her confidence ripped to shreds.
Tamao's pursuit of Nagisa in Strawberry Panic! leads her into downright creepy territory at times, including scaring Nagisa so Tamao can record her screams and watching Nagisa while she sleeps in the very first scene we see her in. Chiyo-chan can get rather strange about Nagisa at times too.
Suki × Suki: Touka is incapable of speaking to Ryoutarou properly when they're face to face. For this reason, the primary use of her invisibility is to follow him everywhere he goes gushing about how much she adores him, comfortable in the belief she can't be seen or heard. Unknown to her, Ryoutarou can see and hear everything she does and struggles despite his discomfort to keep her oblivious.
Sali Tayi from the manhwa Threads Of Time is this way for Atan Hadas. He actually notices when her hairpin (which she gave to Moon-bin as a present of love) is missing, and manages to put two-and-two together remarkably fast (quickly deciding that the best way to resolve everything is to Murder the Hypotenuse). To put it in his words: "I've always been watching you..."
Tamagotchi has Himespetchi, who has a crush on Mametchi. She is very shy around Mametchi, but will still follow him whenever she gets a chance, and she will sometimes walk in on him at the wrong place and time, leading her to think that Mametchi has feelings for another girl. The stalking doesn't go to any creepy lengths, but it still counts.
Tsukiyama from becomes one to Kaneki, blurring the lines between amorous and murderous intentions. He starts out simply intending to serve Kaneki up as the dinner at a Nasty Party, but changes course the moment he realizes that the other is a rare Half-Human Hybrid. Over the course of the story, he goes from simply stalking Kaneki with the intention eating him to becoming his Token Evil Teammate with Yandere tendencies. When he fails to stop Kaneki from going on a Suicide Mission to his apparent death, he falls into despair and enters an Angst Coma.
In the sequel he is shown getting motivation to get over his Angst Coma the second he learns Kaneki/Sasaki is alive and stalking him.
Sasaki theorizes that Torso removes the legs of his victims so they won't "leave". Once he becomes obsessed with Mutsuki, he becomes obsessed with following him and making him his, which especially escalates after Mutsuki responds to his affections in the negative leading to him to cut off his limbs to keep him from leaving. A volume 4 diary entry reveals that he believes they share a mysterious connection, and this "spark" of desire will be his salvation. He just believes they need to have a long, private talk.....then Mutsuki will understand their destined bond, and return his love. After he cuts off Mutsuki's legs and arms he declares he will forcibly marry him while having him dressed up in a white dress and putting a wedding ring on his cut off hand. He then stands in front of him shirtless while breathing deeply which heavily implies Attempted Rape. Usually, his past "lovers" rejection of him drives him to extreme violence to punish them including destroying their faces. Also, in chapter 73 of re: Torso brings Mutsuki a flower crown, but gets angry when Mutsuki glares at him and won't accept his compliments. He beats Mutsuki violently while screaming insults. He later has them on a makeshift bed and says he only beats Mutsuki because of how deep his love for him is.
Romo pining after Kaneki because she thinks he's beautiful when he's in the midst of despair and considering killing Sasaki so he'll turn back into Kaneki.
Eto reveals she has feelings for Kaneki after she sees him maim Tsukiyama and Kanae while invading his personal space and licking him. She's further certain in this fact after he tries to murder and maim her. When he attacks her she also chases him down, and when he cuts her in half she falls while laughing and proclaiming her love for him. A later chapter shows her in a tub thinking and talking about Kaneki, saying she hope his cute hand that Kanae chopped off has regrown and referring to him with hearts in her speech bubble.
Rize falls for Kaneki the moment she notices his good looks and preys on him, mixing amorous with murderous affections like Tsukiyama.
Wolf Guy - Wolfen Crest has the Big Bad Haguro Dou who becomes completely and crazily obsessed with protagonist (and werewolf) Inugami. He initially doesn't care about or even think twice about Inugami... until he pushes Inugami too far. Which results in Inugami showing him his true form and scaring the shit out of Haguro. Haguro goes insane from it, and obsesses and stalks Inugami after that, even cutting himself all over his arm and carving the word "Inu" onto his hand. And yes, it's creepy to the point of being something of a sexual obsession as well - Haguro has been shown after that to, while having sex with his (equally crazy) girlfriend (who, by the way, also lusts after and stalks Inugami and thinks about him while having sex with Haguro), think only about Inugami, and pretty much screams his name while imagining him. Later, Haguro even ends up raping his male subordinate to death, while again thinking of Inugami. And after Inugami decides he's had enough of this shit and tries to move away, Haguro, being the stalker he is, tries desperately to do stuff to piss Inugami off so that he'll come back, up to and including getting hold of Aoshika, Inugami's teacher and Morality Chain, and horrifically raping her.
It was left out of the dub, but Vivian Wong from Yu-Gi-Oh! seemed very much this way towards both Yugi and Kaiba. She had... unhealthy fantasies about them. (She might have eventually crossed the line into a Yandere if Yugi hadn't seriously knocked some sense into her.)
Karasu from YuYu Hakusho. He had been following Kurama around the Dark Tournament... in order to kill him because he loved him so much.
Patie (Penny in the dub) in Zatch Bell!. Her bookkeeper is basically homeless, but she drags him with her to Japan to find Gash. And when he doesn't remember who she is, she flips out and tries to defeat him and burn his book, although she repeatedly offers to stop the fight if they'll remember their love. However, as flashbacks show, Patie was a creepy stalker even in the demon world, and Gash didn't notice her there either because she was always sneaking on him.
Zetsuai 1989: Koji's behavior towards Izumi can only be described as "stalker-ish", like when he turns up at Izumi's football games and buys an apartment across from the field where Izumi practices...