Michelle Flammel from Monsterful, She's in love with the fluffy Rag doll Jacob.
Jacob is also one in the first chapter, he's seen stalking Sapphire.
Damian from Zoophobia harbors an unhealthy infatuation with Kayla, who has a boyfriend, and is incredibly creeped out by Damian.
El Goonish Shive's Justin has one — Melissa, who has stalked him since their one date in High School... which was where he told her he was gay. Apparently, that has not dissuaded her. Since they actually grew up together, she counts as an Unlucky Childhood Friend to boot...
The Gene Mage in Terinu fits this trope for Terinu's race, given a tendency to refer to them as his "sweet limbed Ferin", with an extra helping of creepiness considering he deliberately created them to look cute and perpetually somewhere in their mid-teens.
Eastwood in Exterminatus Now was (or maybe still is) one of these, as he had his ex-girlfriend's new boyfriend put to death by a squad of special forces that are normally used to combat the paranormal. The fact said new boyfriend was actually a heretic only came to light after he was shot to death on the lavatory. Eastwood also seems to be rather overprotective of what she still sends him, such as attacking his associates with an axe after they ate some of the biscuits she sent him.
Autumn became a client of Suicide for Hire because the victim of her stalking publicly humiliated her after she went too far. She tried to murder his new girlfriend.
Namir Deiter: Cedric Van Helgen towards Tipper Namir. His unwillingness to take "Go away" for an answer culminated in his getting punched out by Tipper's fiancee, Charles.
Cassie from The Wotch, with the classic symptoms of obsessively following Robin around, trying to slip him love potions, and other doings of questionable ethics. A recent run-in with her own Stalker with a Crush seems to have made her see her wrongdoings.
Yet another one that seems to have finally gotten somewhere.
Jason was this to Anne at the very beginning of the series, with Robin even noting that "In some cultures, this is considered stalking). Jason drops his crush - and stalking - pretty quickly when he sees Anne levitate a pencil though.
Sinfest neatly encapsulates the trope here, with Fuchsia the succubus's crush on Criminy the shy little nerd. The devil finds this vastly irritating, as it makes her act less evil than she's supposed to be.
Gunnerkrigg Court has Diego. Good lord, Diego. It got to the point where he programmed all the robots he built to worship Jeanne as a sort of Christ figure. And when he gets rejected, he recommends her for a Human Sacrifice. Hell hath no fury like a lonely, big nosed inventor.
At least he didn't tell the robots about that last part, so they still see Jeanne in a positive light. Better than nothing.
Wiglaf & Mordred - Brat. As soon as she lays eyes on Mordred marrying him becomes her goal in life.
Vriska is this to Tavros, although in her case, it's less "spontaneous, unashamed affection" than "I am attracted to him, and that makes me feel uncomfortable...so I have to hurt him for making me feel this way." Evidenced on this page, where she both relentlessly bullies him and tries to make him say that she's pretty.
Persona 3 FTW turns Aigis into one of these for the main character. She was canonically into him in Persona 3 itself, but here it gets taken to "has a habit of humping his leg" levels.
In this strip of Loserz. "I spend all of my time with them, I swear I'll be with them forever *sob*, I hide in their bushes..."
Camp Gay Dillon is prone to sneaking secret photos of attractive, unsuspecting straight men — including Gary, towards whom his behaviour becomes highly manipulative and infatuated for some time. Even when he's in a seemingly stable relationship with Jerzy (in his own comic), he ends up following Jerzy around in disguise.
Zii sneaked away from the possessive and sometimes psychotic Yuki in the middle of the night, but Yuki doesn't take that as a hint. Zii keeps saying that she wants Yuki to leave her alone, but eventually gives up, at least for a while, and has sex with her. While Gary is on a pseudo-date with Yuki. Loudly, all night. While Gary can hear.
Later, Yuki realizes that she's attracted to Gary, and leaves Zii alone. However, once Sonya realizes that she's in love with Zii, she takes over the function. Unfortunately, by then, Zii is trying to maintain a monogamous relationship with Erik. This doesn't stop Sonya, who deduces from Zii's treatment of herself when they first met that Zii didn't take boyfriends seriously (despite Zii's insistence that this case is somehow different), and her actions become increasingly morally dubious as she not only exploits Zii's hot buttons, but also tries unsuccessfully to seduce Erik. She does realise that she had neglected to tell Zii that she loved her as well as wanting her for sex, until it was too late, leading to an odd little Pet the Dog moment (February 19 2013, strip 710, NSFW). But she tends to bounce back from setbacks; this doesn't stop her, and nor does the prospect of competition from DiDi for Zii's affections. She does begin to wonder how she could get past Zii's "playing hard to get", but then Peggy comes to her assistance.
It's a plotline that again belongs more in spin-off comic Sticky Dilly Buns, but anyway, as seen here, Angel is worryingly obsessed with Jerzy, to at least borderline-stalking levels.
And then — new minor character Isabelle initially shows up with just a fangirl/groupie attitude towards Zii, but her interest rapidly becomes quite extreme, probably coming closest to actual, insane, real-world stalking. (The broken lock on the apartment door seems like a real bad sign.)
Isabelle: I need to add her address in my contacts. Do you know her full name? Including middle name, and her mom's maiden name? Gary: S-somehow it's never come up. Isabelle: And do you know her cell number? That would be really useful. Any siblings? Cousins? Pets? What's her favorite food?
Oh Young Gon from Cheese in the Trap is like this to every girl he fancies. It mostly involves giving them unwanted attention, and secretly taking photos of them at school. These girls tend to get him to back off by publicly humiliating him, as only an over-the-top rejection can convince him he's been rejected at all. However Hong Sul happened to show him an ounce of kindness when his latest rejection turned him into a social pariah. He has since been convinced that she secretly loves him, and taken his stalking tendencies to a new level: following her home, sending her unwanted gifts and texts, and trying to behave as though he actually were her boyfriend. Not even Sul threatening to call the police on him can convince Young Gon that she's anything more than shy. All of his recent actions have apparently been part of a plan to get Sul and Jung to break up, and to convince her that he's not a creepy stalker and is actually good boyfriend material. The fact that he has such a plan does not help his case. Nor does following her around the library surreptitiously trying to take her picture. And he still won't take no for answer. Some of this might sound tame compared to other examples, but the fact that everything is played out realistically makes his actions genuinely frightening.
In Inverloch, Arc Villain Berard is an interesting example of this. He used to be a thief-catcher and Lei'ella's boss and once asked her to marry him, which she accepted after an initial rejection; then he rejects her when she reveals she's an elf. When he finds that she's befriended and left with a da'kor (Acheron, The Protagonist) he stalks them and abducts Acheron for a gladiator match, where it becomes clear that he still feels very possessive of her despite having dumped her out of Fantastic Racism, is jealous of Acheron's friendship with her, and becomes outraged when he sees her hug Varden.
The dragon from the prologue of Far to the North seems to have taken an interest in Kelu after she punched him in the face and stabbed him in the gums with one of his own scales. He (or his goblin minions) are apparently now scattering scales around her home disguised as tiny snowmen.
In Girl Genius, Xerxsephnia von Blitzengaard has evidently been acting this way towards Gil since they were children.
In I Love Yoo, Kousuke is constantly fending off Meg, a woman who keeps following him around insisting they're a couple even when he's all but threatening her with a restraining order. Doesn't help that his father seems to be trying to facilitate a relationship.