Esdese of Akame ga Kiru! sees the main protagonist Tatsumi as her perfect ideal man and is blindly in love with him. The problem is she is a completely insane sadist who massacres and tortures people with glee and Tatsumi is a member of a group trying to topple the country she is a leader of.
Road towards Allen in D.Gray-Man. She even kisses him at one point.
In episode 4 of Meitantei Holmes, Professor Moriarty kidnaps Mrs. Hudson to get to Holmes, but she's so kind that he soon develops a serious crush on her himself. When the plan eventually fails, he releases her and promises never to involve her in one of his schemes again.
The whole deal in InuYasha would have NOT started if the thief Onigumo didn't fall in love with Kikyou, then made a Deal with the Devil that transformed him into none other than Naraku...
Also from the same series, Jakotsu towards Inu-Yasha himself, and Mukotsu towards Kagome.
Happens more than once in Sailor Moon, where villains of both genders were attracted either to Usagi (Filler Villain Seijuuro/Alan, Prince Diamond) or to Mamoru (Queen Beryl, Filler Villain Natsumi/Anne, manga!Dark Lady, anime!Fish Eye, anime!Nehelenia).
Creed from Black Cat owns this trope. His crazy rampaging crush on Train is so obvious that everyone notices it... except Train.
This is what Neil Regan actually feels for Candy White Andree in Candy Candy. Near the end of the series we're briefly fooled into thinking this will lead to Love Redeems... but he tries to pull a Scarpia Ultimatum instead.
Also, Neil's sister Elisa has a brief one on Candy's second love interest Terry during the Boarding School arc. He couldn't care less and humiliates her for being mean to Candy.
Rather infamously in Spider-Man Sins Past, Norman Osborn took a shine to Gwen Stacy. And by that it means he impregnated her, then murdered her to get the super-fast aging children.
Actually, the Green Goblin didn't murder her to get the children. Remember, he didn't hunt down Gwen and kidnap her, he captured her simply because she was at Peter Parker's apartment, and wanted to use her as leverage against Spider-Man. Had Gwen been his actual target, he would have gone to her residence.
The Jackal's entire motivation was that he was in love with Gwen Stacy.
Also in Batman, Two-Face had a long-standing obsession with Renee Montoya. While it did lead to her being able to act as his Morality Pet on a few occasions, it didn't end well, partially because of Incompatible Orientation - Renee is very firmly a lesbian.
In the My Hostage Not Yours series, second Big Bad Iggins' obsession with Gaz starts out as wanting revenge, but in the end it seems he's got a thing for her as well, judging by his jealousy of Zim and his actions after he manages to brainwash Gaz into his slave.
The original pulls something of an I Have You Now, My Pretty before his Last Villain Stand, abusing Beth and petting her like a sex slave. (He leaves her virginity intact as a matter of chilling practicality: he doesn't have time before the heroes arrive.)
The clone behaves more like a Stalker with a Crush, outright admitting to Beth's husband, Sherlock Holmes, that he's been keeping an eye on her to ensure that she'll remain a Worthy Opponent. On the whole, he tends to address Beth more than he does Sherlock, apparently as part of his mind games.
Mega Man Recut has Snake Man having a crush on Roll, though he doesn't realize it.
Pictured above: Frollo to Esmeralda in The Hunchback of Notre Dame. The Villain Song "Hellfire" is about his conflict over him lusting after her when she's a gypsy and he's a "righteous" man of the church.
The title character towards Roxanne since before the events of the film, as confirmed by the filmmakers' commentary. Neither of them realize until he starts dating her as his alter-ego Bernard and everybody had assumed she and Metroman were an item (turns out they were Just Friends).
Hal/Titan, who only wanted to be a superhero to get Roxanne's attention. When she rejects him, he turns into a villain.
Jareth to Sarah in Labyrinth. Foreshadowed in Sarah's story to Toby at the beginning: "But the Goblin King had fallen in love with the girl..." He sends her into a dreamlike state featuring a Dance of Romance between them, and at the end, he (albeit slightly ambiguously) offers her the chance to stay with him and be loved by him if she gives up her quest.
Ming the Merciless seemed pretty hung up on Dale Arden in Flash Gordon.
Subverted in The Princess Bride. It appears that Prince Humperdinck is in love with Buttercup, but it turns out that he just wants to marry her so he can arrange for her to be killed and then use her death to justify a war with the scapegoats.
Dark Helmet for Princess Vespa in Spaceballs, from what you can tell in the scene where he plays with his action figures.
Harry Potter: Snape's unrequited love for Lily Evans. Though it's somewhat debatable that he even counts as a villain, seeing as everything he's done in life after Lily's death was to protect her son, Harry Potter. Even if he treated him like shit because of petty jealousy over him being the son of James, who was The Rival to him.
Spike from Buffy the Vampire Slayer has this trope down to a tee. When he first (canonically) falls for Buffy, he's still in total opposition to her and the Scoobies' goals, and yet is blatantly head over heels for her. Buffy's mom asks if she might have lead him on unintentionally, to which Buffy replies that she beats him up a lot. Which for Spike is pretty much the same thing.
Yet again to Kurt's misfortune, Season 3 introduces Sebastian Smythe, who is adamant on taking Blaine, Kurt's boyfriend, for himself.
On Heroes, even though he already taken her power, Sylar appears to have a creepy thing for Claire.
On Luther the eponymous detective has to deal with the uncomfortable fact that his closest friend and confidante, and most reliable source of help is Nietzsche WannabeManipulative Bastard and thorough psychopath Alice Morgan. That alone would be bad enough, but as many of Alice's lines suggest, she may well have a thing for Luther.
There were indications in Season Two that how Lord Zedd felt about Kimberly in Mighty Morphin' Power Rangers was not just Foe Yay subtext, especially with the episode he tried to make her his queen.
A filler episode of Power Rangers Ninja Storm suggests comic relief villain Choobo had one on Tori, the only female ranger on that team.
Murdoch Mysteries: It's implied that the young psychopath James Gillies is attracted to Detective William Murdoch after the former kisses the latter on the mouth for a full three seconds in "Midnight Train to Kingston." It has been hinted throughout the series that Gillies is gay, and it seems natural that he would be drawn to a handsome, intelligent man like Murdoch. Robert Perry, who was presumably James' boyfriend in an earlier episode, is somewhat similar to the detective in that he was also dark-haired, comely, mild-mannered and smart.
Lionel's unrequited crush on Martha which ran for most of the show.
Appears to be the case with Michael in Stargate Atlantis. Since Teyla was the only person to treat him nicely during his introductory episode, Michael becomes attached to her and, even after she has betrayed him repeatedly (in his own words), he still hopes he can convince her to come away with him.
Katherine for Stefan and also Matt, although she never does more than talk about how hot he is.
Ares has it bad for Xena: Warrior Princess, to the point where his motivation throughout the show is to win her love.
In Ring of Honor, Jimmy Jacobs has it bad for good guy Adam Cole. He's open-mouthed kissed Cole on at least one occasion, and taking this to an unusually meta level, has propositioned Cole for sex on Twitter.
Shadowrun adventure Harlequin's Back. In the backstory, a Horror fell in love with Queen Thayla and refused to leave her, even though his presence was destroying her land. She eventually decided to leave with him to save her people from destruction.
Judge Turpin of Sweeney Todd: The Demon Barber of Fleet Street developed two of these. The first was on Sweeney's wife, Lucy Barker, which ultimately led him to kick off the plot by having Sweeney transported for life, followed by luring her to a masked ball and raping her. The second was on Sweeney and Lucy's daughter Johanna, who he adopted out of remorse for what he did to Lucy but came to desire as more than a daughter as she grew older.
Mrs. Lovett has one for Sweeney Todd himself, though they're both more Villain Protagonist than heroes.
Jud for Laurey in Oklahoma!, though how much one considers Jud to be a villain is up for debate.
Darth Sion of Knights of the Old Republic II developed an interest in the female Exile immediately after seeing her; his crush was so intense, it was threatening his connection to the Dark Side, and therefore his life.
In Final Fight Revenge, Mad Gears member Poison develops a crush on Cody, and visits him in jail (despite the fact it's her fault he's there because she framed him). Note that this was before the official confirmation that Poison was a post-op transsexual, but it was still rather bizarre. (She acts very feminine in this particular game.)
Fire Emblem Jugdral: Apparently, King Travant had some feelings for Sigurd's younger sister Ethlyn. Too bad she was already Happily Married to Duke Quan. And even worse: Travant later killed them both in the war and took their daughter Altenna into his household so she would use Quan's signature weapon, the Gae Bolg, for him.
In Immortal Souls, the crazy vampire the Black Witch is very much into the hero John, openly flirting with him every time they meet. It's implied the attraction is why she turned him into a vampire, and IsisCorporation also "recruited" John mainly so they could use her attraction to their advantage. John is pretty squicked out by the whole deal (mostly understandably pissed off she turned him), but does take (non-sexual) advantage of the matter sometimes.
Ghosts are typically the most common antagonist in Pac-Man but that doesn't stop Pinky from having a crush on Pac.
In Girl Genius, maybe Zola was faking weakness every time Gil had to rescue her, but her love for him remains after she revealed being way more dangerous than she looks.
Depending how you interpret him, Tarvek may be this (crush undisputed, villainy not certain). And Gil, but he's rather an Anti-Hero. Given that all four characters thus mentioned are very powerful and not strictly aligned players in European politics, Friend or Foe becomes a complicated question.
Princess Attea towards Ben in his Inkursian form Bullfrag in Ben 10: Omniverse. To Ben's chagrin, the feeling is mutual as Bullfrag.
Agent Bishop is very affectionate towards Karai when he has her captured in the 2003 Teenage Mutant Ninja Turtles, spending half the episode kicking the asses of Hun and the Turtles, and the other half admiring Karai and going on about how lovely she is.
In one episode of Teen Titans, Red X flirted with Starfire after pinning her to the wall with one of his gadgets, calling her "cutie" and remarking that the "only crime" between them was that they hadn't gone on a date. (Her only response was to blast him with her starbolts through her eyes.)