Gender-inverted in Codename: Sailor V (of which Sailor Moon is a spin-off): in the end it's revealed that the Big Bad Danburite AKA Ace is in love with Sailor V since their previous lives. Even the eventual failure of this is unusual: she does fall for him, but everything he did was to get Minako to fully awaken as Sailor Venus and make her realize she'd always choose duty over everything by having her kill him.
While Slan of the Godhand in Berserk is probably incapable of feeling real love (being a God of Evil and all), she does want to make Guts her personal sex-toy.
From Anpanman, Dokinchan, Baikinman's second-in-command, has a (very large and very obvious) crush on Shokupanman, one of the members of the breadheaded superhero team. He's a bit too conceited to notice her crush, though he treats her with a level of kindness that he doesn't show any of the other villains...besides Dokinchan's little sister, Kokinchan, who ALSO has a crush on Shokupanman (though hers is a bit more of a childish one, and she's treated as less of a villain by most of the cast).
In D.Gray-Man, Road, the Noah of Dreams, has a 'thing' for Allen Walker...though pretty much everyone does. However, this infatuation seems to be a source of Character Development for her, as she becomes nicer to Allen...though only to him.
There's also Hela, Norse goddess of death, who is either this or a Stalker with a Test Tube, Depending on the Writer. She's also Thor's adoptive brother's daughter, by the way, but mythological gods have never been exactly picky about that sort of thing.
The Enchantress' younger sister Lorelei also wants a piece of thunder god, and once used magic to seduce and rape him.
In the "Den" segment of Heavy Metal, the evil queen really wants to get it on with the eponymous hero. And then they actually do get it on.
Films — Live-Action
In Star Trek: First Contact, the Borg Queen wanted Picard to willingly submit to the Borg and be her..."consort"? Not technically romance, but the Borg Queen seems to sexualize her role. The seduction part is played straighter in regards to Data, our favourite fully functional android.
This is the plot of She.
Medusa, the main villain in the last 3 Ninjas movie, offers to spare Dave Dragon if he agrees to be her "boy toy". His rejecting the offer pretty much makes her act less like this the rest of the film.
300: Rise of an Empire: After Artemisia's Persian generals fail to live up to her demands, she takes an interest in her Athenian opposite Themistocles. She summons Themistocles to her command ship to seduce him, prompting a very violent sex scene. He refuses with a simple "No" afterwards.
The Seven Realms Series plays it straight with Han Alistar and Fiona Bayar. The Bayar family is a corrupt family of Wizards that has it out for Han, since Han accidentally wound up stealing a powerful magical artifact from them. Han is also a Chick Magnet of epic proportions whose good looks almost never go unnoticed by a female member of the cast. So, naturally, Fiona Bayar gets the hots for him and even attempts to seduce him by saying they can rule together.
In The Last Apprentice, witches seem to really like spooks, even though a major part of a spook's job is hunting witches. Both Tom and his master, Mr. Gregory, have at least one witch who fell in love with them.
Older Than Dirt: This trope goes back to The Epic of Gilgamesh. The capricious goddess Inanna (Ishtar) wants to hook up with the hero, Gilgamesh, because he's exceptionally comely. But he wants no part of it because, as he points out with brutal candor, every single guy she's ever spent time with lived to regret it (and usually didn't live to regret it for very long). Result? Goddess rage.
His reason for rejecting her is entirely different in the oldest Sumerian version, where his Mother tells him that a relationship with her will make him Soft.
Howl's Moving Castle: The Witch of the Waste's love interest is the wizard Howl, who tries to escape from her in fear.
Lanfear's interest in Rand al'Thor in The Wheel of Time is almost a textbook example of this trope, even down to the We Can Rule Together. She never technically kidnaps him but she certainly does everything she can to make him dependent on her (and, to her credit, she really does save his life more than once).
In the original version of Spider-Man: Turn Off the Dark, the villainous Arachne had a thing for Peter and wished to seduce him away from Mary Jane. When Julie Taymor was fired and the musical was rewritten in order to save it, the subplot was cut as Arachne was Demoted to Extra.
Mass Effect: Aria T'Loak backstory reveals that this was the case when she dated Nyreen, who "oozes virtue" according to Aria. The relationship failed when they both realised that they couldn't make Dating Catwoman work without changing the other. Likewise implied with a subtle undercurrent of Belligerent Sexual Tension in conversations between Aria and Paragon Shepard.
In Kingdoms of Amalur: Reckoning, in the House of Ballads quest line, the Maid of Windemere kidnaps King Wencen of the Summer Court to be her lover, leading to him having to be saved by his queen in the tellings of the ballad before the arrival of the Fateless One.
Used in a minor way in The Order of the Stick. Fairly early, Elan gets kidnapped by bandits who, as it turned out, were acting on the orders of the beautiful Bandit Queen. I guess that 18 Charisma wasn't just for show after all... (Well, it is, obviously, but... you know what I mean.) Somewhat unusual in that Elan actually goes along with it until his UST-target shows up and complains, at which point he defends himself by claiming that seducing the beautiful villainess is part of his solemn duty as a Bard.
There's also the situation between Durkon and Hilgya. Deconstructed in that while she was attracted to him, and he eventually returned the favor, she was still married, and the Lawful Good Durkon could not be involved in a relationship with someone who was married to someone else
I will not bed the Hunky Hero before my plan is executed, unless having him believe I am carrying his child gives me a decisive advantage.
I will not be put off by the Hero's rebuffs of my sensual advances. If he doesn't succumb to me, I will not fly into a jealous rage. Instead, I'll shrug my shoulders, send him on his way, and have him picked off as he exits the fortress.
I, and my elite guards, will never assume that we have managed to confiscate all weapons or escape aids from the captured Hero. "Interrogations" in my private chambers will only be conducted if the Hero is completely nude. This will, in fact, satisfy a number of objectives at once.
However insatiable my appetites are, it is virtually guaranteed that at least one of my millions of subjects is both far more gifted at satisfying them and far more loyal to me than the Hero who seeks my destruction, no matter his reputation with the ladies.
If the Hero has an evil twin, the twin will probably make a far more suitable Love-Happy Stooge.
Flipped around in "Atopthe Fourth Wall", where heroic champion of the universe Linkara has a crush on Harley Quinn, a comic book villainess.
Star Wars: The Clone Wars features Miraj Scintel, the Queen of Separatist-aligned Zygerria, taking a liking to Anakin Skywalker posing as a smuggler to free many recently abducted slaves from her clutches, and, subsequently, after his ruse is discovered, takes Obi-Wan, Ahsoka and Rex as captive slaves, but promises to release them if he would become her lover and stay with her, believing she can control him. Unfortunately, Count Dooku doesn't approve...
Subverted. She just wanted to use Robin to make her real boyfriend jealous.
Blackfire flirts pretty heavily with Robin in her first appearance, but this seems less to be actual interest and more just her screwing with her sister Starfire's (Robin's canon Love Interest) head. In her second appearance, she pretty much ignores Robin entirely.
This trope is played entirely straight in regards to Jinx and Kid Flash though.
Actually, it's completely inverted. Kid Flash is definitely the active pursuer in the relationship, with him trying to coax Jinx into turning over a new leaf.
There was also Saleen, an evil mermaid who attempted the same thing. Though in one episode she turned Aladdin into a shark, which seems sort of counterproductive to this trope.
Both Black Cuervo and her mother Voltura have this for El Tigre and his father, White Pantera. A good way to get Voltura riled is to point out that was Pantera who broke up with her; "As if I could forget!"
In an episode of SWAT Kats, a villainess air-pirate named Turmoil, would develop a crush on the hero T-bone. She would capture and ask T-Bone to join her crew. T-bone would take advantage of her hospitality, planting bombs throughout the ship bringing it down. At the end of the episode, Turmoil, while in prison, promises not go give up her pursuit of T-Bone.
In Avatar: The Last Airbender Ty Lee hits on Sokka almost every time they share the screen together. Of course, she's not really that much of a villain, but she's Azula's sidekick and usually hits on him while they're fighting.
In ReBoot Hexadecimal sometimes had a crush on Bob, depending on which mask she had on at the time. After she's turned into a sprite she comes to realize she loves him entirely and ends up sacrificing herself to save the entire net from Daemon's infection, for no reason other than for his sake.
In Young Justice, Cheshire flirts with Red Arrow's clone. They eventually get married and have a daughter.