There also is a one-sided romance between Quiche and Ichigo, with the former being madly in love with the latter. His love gets creepier as the show goes on... until the end when Quiche refuses to kill Ichigo and gets killed himself. Ichigo is genuinely upset by his death. He gets better, though.
In UFO Robo Grendizer -one of the Mazinger Z sequels-, Duke was engaged to Rubina, daughter of Big Bad. They loved each other. However he did not think they could be together again after what the Vegans had done to his homeworld.
Dragon Ball Z does this twice, though both times the aftermath is shown rather than the circumstances of their falling in love. The first to do this is Bulma, who, over the course of three years, has a relationship with former warrior prince and The Starscream to the previous Big Bad, Vegeta. Interesting in that a time traveller tells the hero this will happen before it does, which knocks him on his ass. The second instance is Krillin, who falls in love with former troubled enemy cyborg #18. After a time skip of seven years, it's shown that they got married and had a kid (remember, cyborg, not android...) In both cases the relationships contribute to a Heel-Face Turn (though #18 arguably had already essentially switched sides by then; it was more of a Loner Face Turn), and both formerly villainous parties act the same way: they don't show it much, but they actually care.
In Special Duty Combat Unit Shinesman, Matsumoto, a young businessman who is secretly a superhero protecting the Earth, accidentally sees a bare skin of Princess Sheena, one of the villains from the Planet Voice who are trying to conquer the Earth. Due to the rule of Planet Voice that whoever sees bareskin of the royalty must either die or marry the royalty, Matsumoto and Sheena start dating, unaware of each other's secret identity.
In the manga, Sheena didn't exist, so this incident happened between Matsumoto and Sasaki/Prince Hope instead. Sasaki definitely embraces the 'kill him' option until the very end of the manga, when he tells Matsumoto he's changed his mind.
Team Chef Sai Saici and Plucky Girl Cécile (the sister of Gundam Fighter Hans Holgar) in G Gundam. Causes less problems than most examples, since Hans is no mortal enemy, but a decent, friendly Worthy Opponent in a sports tournament.
Happens in Red Garden when Kate ends up dating Hervé, a member of the family responsible for the wild men she and the other girls fight. She's oblivious about his real role in things, but he knows hers from the very start.
Superior has this as its premise. It opens with the Demon Queen, Sheila, falling in love with the hero sent to vanquish her, Exa. She conceals her true identity - although he suspects, he cannot bring himself to confront her and doesn't want to believe it.
There are hints that Hayato has some form of romantic attraction (or at least deep respect for) Keith Violet in Project ARMS, although it seems to be mostly one-sided. Keith Green also falls for Katsumi, although again it's one-sided (she has no idea.
Ruby and Courtney from Pokémon Special form a strange relationship as time goes on, eventually leading them to team up against Kyogre and Groudon. Ruby does eventually care for her in a platonic manner, but Courtney definitely feels something stronger for him. Kinda creepy considering he's 11 and she's assumedly in her late-teens/early twenties. Heck, she even went so far as researching his background! (Though that did lead to her discovering information that made realize all that his father sacrificed for his sake).
Bizarre example in The Lucifer and Biscuit Hammer, where the two people are technically on the same side at the present due to an Enemy Mine, but nevertheless one wants to destroy the world and the other wants to save it.
Snake Knight: If, at the very end, I win and stop the two of you [from destroying the world], would you go out with me?
Lizard Knight: I... I'll think about it.
By the end of the series, the relationship between the Lizard Knight and the Princess becomes something akin to this when he decides that he won't let her destroy the world because he loves her. She's actually happy that he's trying to stop her.
In Robotech, the Zentraudi ace pilot Miriya Parino falls in love with Terran ace pilot Max Sterling, after literally engaging in several duels and stalking him with intent to murder. They marry and have a child, Dana, who goes on to pull something of the same thing with the Robotech Master ace pilot Zor Prime (a clone of the original superintellect Zor).
Akame ga Kiru!: Esdese is truly and completely in love with Tatsumi. Esdese just happens to be an insane sadist working for an extremely corrupt government and Tatsumi is a member of a rebel group trying to topple said government. Well Esdese is unaware of this fact, Tatsumi tried a Love Redeems on Esdese more than once, trying to use her love for him to make her become good, but gave up quickly when he realized Esdese is completely insane and can't change.
Naturally, the Trope Namer and most famous example is the romantic tension between Catwoman and Batman. The Earth-2 versions of the characters actually married and had a kid, the original Huntress. Why bother stealing when you're married to a multimillionaire? The main versions became a couple too, and Bruce even revealed his identity to her and she moved into the mansion with him. The relationship didn't last, but they both developed a respect for each other and Batman mostly looks the other way when Catwoman does her thing.
However, things got a bit more interesting with the two. Continuing to dance around one another constantly to the point of a nearly functional relationship, then to a distant one due to fear of repercussions from their knowledge of one another's identity, the couple have certainly reheated things a bit since Bruce's return to the present... long story. Regardless, she has even accompanied him on his international travels to establish Batman Inc. Maybe not a perfect relationship, but hey.
Unfortunately for those who may have enjoyed it, all that Character Development in their relationship has been set back to square one with the 2011 DC Universe reboot, in which Catwoman has no idea who Batman is behind the mask (although she suspects he knows who she is). Doesn't stop her from having costumed sex with him though.
Funnily enough, the whole 'dating Catwoman' trait stems from the fact that Batman himself has a weakness for villainesses, which he acknowledged in Batman R.I.P. His relationship with Talia al Ghul in the main continuity (where they have a son together) is similar with his relationship with Catwoman.
In Gotham City Sirens, it was mentioned that Catwoman and Talia are probably the only two women Batman has truly loved. It's not surprising that both of them are villainesses.
Very explicit in one standalone strip called "Date Night"; Batman catches Catwoman in the middle of a robbery and chases her through various romantic locations including a flower stall and a fancy restaurant, all the while Catwoman is talking and flirting with him as if they were actually on a date. When he finally catches her, they briefly fight and she leaves him tied up and dangling upside down from a fire escape, kisses him goodnight and runs away.
In Batman the Dark Knight after the 2011 reboot, Bruce is attracted to Jaina Hudson, but becomes suspicious of her after new villainess White Rabbit issues the same "Catch me if you can" flirtatious challenge Jaina made in their first meeting. His suspicions are debunked when the White Rabbit shows up on the radar while he is on a date with Jaina. It turns out he was right after all, since Jaina has the power to split herself into two people — her normal self and the White Rabbit.
Spider-Man and the Black Cat fit this one like a glove, though that relationship took second place to Mary Jane, who Spidey eventually married.
Though that particular possibility has now been reopened, due to a Cosmic Retcon. Furthermore, Felicia actually stated on more the one occasion that Peter's marriage vows meant absolutely nothing to her. The second she sees an opportunity to talk him out of his tights, she's taking it.
Captain America dating Diamondback, a member of the Serpent Society (a group of snake-themed supervillains). This is a somewhat defanged (no pun intended) instance, as Diamondback offered to drop crime for him practically in their first meeting. (Not that she came off all that convincing, but...)
The Mighty Thor and The Enchantress (Amora), a goddess of Asgard, who spent years hatching plans to harass and seduce the god of thunder. He eventually relented and had a brief romantic relationship with her.
The Golden AgeGreen Lantern, Alan Scott, not only fell in love with the villainess Thorn, he had children with her. Then again, he did fall in love with her good personality, Rose. His second wife, the Harlequin, also started out as one of his adversaries, although she was long reformed and retired by the time they married.
Making this trope happen is actually the entire reason Harlequin turned to crime. She wanted to catch Lantern's eye, and decided that donning a sexy costume and alternately stealing things and teaming up with him would be the best way to attract his attention.
Likewise, the Silver Age Green Lantern, Hal Jordan, had Carol Ferris (whose Star Sapphire personality made frequent appearances) as a long-time love interest.
His successor as Atom, Ryan Choi was dating Giganta. It was apparently a serious enough relationship that she took vengeance on his murderer.
DC's Roy Harper (a.k.a. Speedy/Arsenal/Red Arrow/whatever they're calling him this week) was sent in to seduce batshit insane assassin Cheshire to get enough evidence to take her in. However, they fell in love with each other and Roy realized he wouldn't be able to do it and walked out... not knowing Cheshire was pregnant. Cheshire herself didn't find out who Roy was until it was all said and done, and then arranged for Roy to get permanent custody of Lian. Cheshire is also the victim of emotional blackmail because Mockingbird put her on the Secret Six by threatening Lian with an explosive device he supposedly implanted.
Of course she DID conceive a replacement child in order to get out of the Six with no hesitation.
Superboy (1990s clone version) dated New Goddess Knockout, under the impression she was a well-meaning thrillseeker, rather than a murderous sociopath.
Superman had a sexual relationship with New Goddess Amazing Grace. And Maxima. Oh, and he married the Kandorian Lyla (he had amnesia).
Witchblade bearer and cop Sara Pezzini and Darkness bearer and Mafioso Jackie Estacado are rivals in their professional and supernatural lives, but as of First Born they have a daughter, Hope, together.
When inept superheroine Empowered met Thugboy, the love of her life, she was tied to a chair and he was part of the gang holding the hostage she was attempting to rescue for ransom. He whispered a few words of encouragement into her ear... and pulled her out of the way when one of her idiot teammates brought the building down. Empowered then lets herself get captured by his gang several more times just to have an excuse to keep seeing him. He does a Heel-Face Turn a few chapters later.
In Johnny Saturn, Johnny Saturn I is married to Persephone, the daughter of Saturn's arch-enemy, Dr. Synn. Persephone is morally ambiguous, and as likely to use her powers to aid her father as her husband.
Subverted with the Ireyon in Paperinik - she comes onto our masked hero because she thinks he is Fantomius, her old flame, whose style and equipment Donald uses for regular superheroing. Donald isn't that interested, and vaguely annoyed she thinks he is as old as his grandpa. (She, on the other hand, is Really 700 Years Old.)
Greyshirt of Tomorrow Stories has Lapis Lazuli. He really does love her, but, well... if they ever got together in any meaningful way, she'd probably kill him the second it went sour. Even she thinks so.
Huntress and Catman had an on and off relationship ever since they fought for the first time. While it never got further than intense Foe Yay, they still cared deeply for one another. Huntress never stopped hoping Catman would be redeemed, and Catman for his part appreciated it even though he believed he was beyond redemption. Catman enacted a ridiculously complicated scheme to make Huntress give up on him because he wanted her to be happy with someone else. Catman had just been through a Trauma Conga Line that convinced him that he didn't deserve anyone's love, least of all Huntress'.
Karolina Dean of the Runaways first encountered her current girlfriend Julie Power back when the latter was part of a group that had been organized specifically to shut down the Runaways. They later hooked up after Julie's then-employer Hank Pym tried to kidnap Molly Hayes and Klara Prast.
It is revealed in Watchmen that Night Owl II had a fling with Twilight Lady.
Not just the yaoi. Even if a character in Detective Conan isn't a detective or affiliated with the police, they still usually have a thing for following the law, which means that pretty much any pairing involving Kaito is this, including his canon pairing.
Happens a lot in Pokémon fanfiction, where it seems like every generation has had at least one popular ship pairing a rival (or even villain) up with a hero. The ready supply of attractive villains probably has something to do with this.
All You Need Is Loveships Light and Naomi. They have "Victory Sex" once and Naomi ends up having Light's child, which she conceals from everyone. And that's the most normal thing that happens in that wonderfully bizarre and light fic.
Lampshaded in Fever Dreams when L gets him and Light some matching tracking devices which he uses when he keeps Light under house arrest and nicknames them "the wedding bands."
In Shadow Snark Twilight Sparkle and Uma o Henko Suru a changeling
Frequently crops up in Glee fics. Usually a member of New Directions starts dating one of their bullies or someone from a rival glee club.
A good fifty percent of all Kim Possible fics seem to be focused on KiGo... that is Kimmie and Shego becoming an item... and like as not having kids and getting married... sometimes in that order.
In Voldemort Goes Back To School, when Voldemort (in the body of a teenager) infiltrates Hogwarts as a new student in the hopes of killing Harry, Hermione notices that the new Slytherin kid keeps sending Harry "heated stares" and comes to the conclusion that he has a crush on him. Hilarity Ensues.
There is plenty of fanfiction that tends to pair Danny with Ember Mc Lain.
Films — Animated
The Incredibles: Mirage and Mr. Incredible (though the extent of their relationship is very unclear). Of course, the fact that Mirage ends up apparently turning good anyway and helping the protagonists makes it more questionable. Really only a partial example as they were never really in a relationship (Mr. Incredible already being married and Mirage respecting that.), but their flirtatious banter, while standard for superheroes, did have strong subtext of being an emotional affair on his part.
One of the DVD extras is an explicit reference to this trope: In the background info on the Supers, there's an audio clip where The Casanova Gamma Jack describes how difficult it is to fight attractive female supervillains.
In Metropolis, Freder is the son of the semi-evil Capitalist overlord, and Maria is a young Socialist reformer. It turns out okay, though.
Out of Sight involved a romance between George Clooney's gentleman bank-robber character Jack Foley, and Jennifer Lopez's US Marshal character Karen Sisco. Notably, in a change from the novel, Karen appears to deliberately plant an escape artist in Jack's prison transport so she can keep chasing him.
DEBS: both the short and full-length versions of this film center around a secret agent's forbidden Les Yay romance with a supervillainess.
Amy: If you'll excuse me, I have a date with the devil.
Most James Bond movies include some sexual tension with any female antagonists present (or at least the attractive ones), but in most cases, it's either part of the villains' plan to kill Bond, or the ladies became good when the Big Bad mistreated or betrayed them. From Russia with Love, Goldfinger, and Live and Let Die are the only ones where the henchwoman genuinely becomes a love interest.
The Dark Knight Rises has this dynamic from early in the movie as Bruce shows a far more playful tone with Selina than his other enemies. Over the course of the movie their mutual attraction slowly develops and they ultimately end up creating new identities and leaving Gotham together.
Batman Returns, which makes Catwoman a good bit more sympathetic, if somewhat more insane (she's more in the crime business to get revenge on her murdering boss and knows she can't live with herself when it's over).
Catwoman has Catwoman and Tom Lone, though it's more between her "good" civilian side (when she tries to make moves on him as Catwoman, she is rejected to "I'm already seeing someone").
Batman XXX has Batman and Robin "dating" Catwoman.
Sherlock Holmes and Irene Adler definitely have an air of UST and Irene kissed him at one point (though he was drugged). Most Holmes adaptations follow this portrayal, although the original Irene Adler of "A Scandal In Bohemia" was technically not a criminal.
In the second film, they kiss again and arrange a dinner date. Holmes is later shown to be quite despondent over her death at the hands of Moriarty, and adds revenge to his motives for going after him.
This would have been the premise of the unmade Romance of The Pink Panther, which was ultimately scuppered after lead actor/co-writer Peter Sellers died: Inspector Clouseau falls in love with a woman who's actually the Classy Cat-Burglar he's trying to capture.
The plot of Entrapment is based almost completely on this trope.
Warren Peace, an Anti-Hero type character in Sky High is a product of such a pairing.
Lifeforce. The astronaut protagonist is obsessed with the beautiful space vampire he is hunting, even though to touch her means death. They nevertheless make out several times. There's even a Ho Yay moment when he's driven to kiss her while she's occupying the body of a man. He later discovers the reason for his obsession is that she took the image of the perfect woman from his subconscious.
Corran Horn and Mirax Terrik of X-Wing Series. He's a former space cop turned pilot. She's a smuggler. His father was the one who finally landed her father in jail. Still, she's a smuggler on the Rebellion's side, is like a sister to his commanding officer, and doesn't smuggle anything too nasty. They make it work. Even if her father objects strongly.
The later Wraith Squadron books have another one between Myn Donos, the Wraiths' sniper who lost his whole squadron in an Imperial ambush, and Lara Notsil, really Gara Petothel, an Imperial spy who planted the information attracting them to the ambush. After flying with the Wraiths in disguise for a while she ends up Becoming the Mask and falling in love with him. She's forced to fake her death, but Mercy Kill reveals they eventually found each other and are Happily Married with children.
Luke and Mara in The Thrawn Trilogy and, of course, Hand of Thrawn. He's the last of the Jedi, she's the former personal assassin of the Emperor who wiped out the Jedi. Then he rebuilds the Jedi and she becomes second in command of one of the largest criminal organizations in the galaxy. Of course, despite the Jedi theoretically being keepers of law and order, said criminal organization ends up being one of their most reliable allies and gets less and less criminal as time goes on.
And of course, their son Ben may perhaps become involved with a Sith girl, Vestara Khai. There's certainly high amounts of UST. Bear in mind that the Jedi and Sith have existed largely for the specific purpose of opposing each other for thousands of years, and ultimately the conflict dates to before either order actually existed.
There's the fan-favorite of the demon Crowley and the angel Aziraphale in Terry Pratchett and Neil Gaiman's Good Omens. They're Mistaken for Gay in the book, and Word of God is that they end up sharing a cottage in South Downs. Not quite a textbook example, as by the time of the book they've decided they have more in common with one another than either of them has with his respective boss, and have an Arrangement. In addition, this is more like Asexual Life Partners, due to the very nature of angels and demons.
Played straight with Anathema, who's a witch, and Newt, who's a witch-hunter, albeit a not-very-enthusiastic one.
In Harry Harrison's Stainless Steel Rat series, the first novel that introduces Angelina gets like this. At first, Jim only wishes to catch her for his boss Inskipp. After all, it's not a very good idea to have a crazy murderess flying around in a giant battleship. After he foils her initial plot, she tries to kill him. He then gets a disguise and finds her again, running a con on another planet. While in this disguise, he starts to see a different side of her. He saves her from an assassin, and they end up spending the night together. She later reveals that she knew who he was but didn't care anymore. After some psychiatric help to remove her homicidal tendencies, they end up getting married (although it's literally a Shotgun Wedding), thus the following novels no longer fit this trope.
Tawnos and Ashnod from The Brothers' War (Magic: The Gathering) are in love, despite being generals on the opposing sides in a war.
The only woman Hercule Poirot comes close to being romantically involved with, is a highly skilled jewel thief.
In The Three Musketeers, d'Artagnan dates Milady for a while. And really, he is the one who lies to her.
Lymond Chronicles ... Where to begin? There is the cringe-inducing tension between Lymond and ex-from-Hell Margaret. And his night with Joleta, where it is typically ambiguous who is seducing whom. ("There is such a thing as seducing in hate".) And perhaps Guzel.... And.... And....
Inheritance Cycle: Nasuada and Murtagh. Their attraction sparks when Murtagh is a prisoner of her father, which blossoms into serious feelings when she's captured by his master Galbotorix.
In Ayn Rand's The Fountainhead the "hatred" between critic Dominique Francon and architect Howard Roark becomes proverbial, and newspaper commentators compare it to "A Medieval vendetta." She writes articles condemning his buildings and uses all her charm to dissuade people from giving him a job. Nobody knows (though they live in New York City and are both much in the public eye) that they spend their nights together. In bed she tells him what she had done that day to destroy his career, and he laughs - knowing this is her way of showing that she really loves him. The two thoroughly enjoy acting like arch enemies in public by day and being secret lovers by night.
In Rand's Atlas Shrugged the protagonist Dagny Taggart spends half the book searching for a man she calls "The Destroyer" and "The Most Dangerous Man Who Ever Lived", vowing to save the world from him. When she finally finds him (the famous John Galt), she falls in love with him at first sight, but still tries all she can to thwart him for another quarter of the book. (Rand's posthumously published Journals include a planned scene where she actually hands him over to the police and then bursts out crying when he is taken away; in the actual book, she only pretends to do it in order to save his life).
In Jack Vance's Lyonesse trilogy, the protagonist Aillas falls in love with the haughty viking-like maiden Tatzel while being a slave at her father's castle. He escapes, comes back as a warrior king, kidnaps her and undergoes many adventures together with her, saving her life several times. Throughout he acts as the perfect gentleman, not taking advantage of his power over her. At one moment she actually offers him sexual favors in exchange for her liberty - but Aillas, wanting a love she is unwilling and unable to give him, declines the offer and sets her free anyway. Finally, when Aillas brings his army to assault the castle, Tatzel takes up a bow and arrow and dies among the last-ditch defenders. The victorious Aillas sadly refuses to look for "the body of the valiant maiden" among the scorched bodies in the ruins of the castle, and goes on to find another and more rewarding love.
Almost every Sherlock Holmes work not by Arthur Conan Doyle, from professional novels to amateur fanfics, has this crop up between Holmes and Irene Adler, to varying degrees of intensity and success.
Occurs in the first two books of the Elemental Assassin between the protagonist Gin and Detective Donovan Caine. While he eventually loosens up on the fact that she killed his partner (Ultimately coming to the conclusion that if he'd known how dirty his partner was, he might have killed him himself), the basic fact that she's an assassin and he's a cop creates a conflict that they're never quite able to get over despite their mutual attraction, and Donovan ultimately removes himself from temptation by transferring to a different city.
The novel Never Leave Me by Margaret Pemberton takes place in Nazi-occupied France, and its plot features a French girl who is active in the Resistance and a German Wehrmacht officer who fall deeply in love with each other. Much against both of their wills and in complete contradiction to the mutually-antagonistic national causes both of them serve, they are helpless to stop their intensive attraction to each other.
Happens in The Stone Prince in the middle of a battle, to the point where the man retires from combat to let his hormones settle before going after the woman again.
The Committee of Public Safety of the People's Republic of Haven in the Honor Harrington series of novels assigned Political Officers to watch over its captains and admirals, as they were terrified the Navy might try a coup. While some People's Commissioners developed a wary sort of friendship with those they were theoretically supposed to ride herd on, most did their best to generally make their assigned captain/admiral's life a living hell. Unfortunately for the Committee, though, one of those commissioners and her admiral wound up falling quite desperately in love with each other. Though the two maintained a facade of icy hostility in public, as the commissioner in question was trusted implicitly by the Committee and thus could use her position to her own ends, behind closed doors was quite a different matter. In the end, with the help of a few other key Navy personnel and their collaborative commissioners, they ended up overthrowing the committee and restoring the Republic of Haven.
Live Action TV
Dark Angel has Max and Logan meet after she steals his priceless Egyptian cat statue. He's the rich-hero-by-night ("eyes only") and she ends up helping him solve crime
Captain Picard and archaeologist/thief Vash in Star Trek: The Next Generation. Also, Captain Sisko and Kasidy Yates in Deep Space Nine (Although the fact that Kasidy was a smuggler doing business with The Maquis was as swiftly ignored as it was tacked on). There's also Odo and the Female Changeling from Deep Space Nine.
Teen Wolf: Scott and Allison. A variation in which he knows she's on the opposing side, or, that her father is anyway- Also, starting season 3, Danny and Alpha Twin Ethan in a homosexual and supporting character version of this.
Jack and Nina from 24. Though all tension is gone from Jack's end and replaced with genuine hatred once Nina kills his wife.
Smallville, in the first of the three episodes Alicia appears in, the Clark/Alicia relationship is this trope. Afterwards, she's Reformed but Rejected by all but Clark. And in Season 7, Oliver/Tess, though they only dated before they became hero/villain, and besides one booty-call, nothing else happens.
Nikita. Michael and Nikita are on opposite sides, but used to work together. Sometimes it's subtext - their inability to kill each other - but sometimes not so much. By the end of the first season, Michael's switched sides, so this trope no longer applies and they revert to being a Battle Couple.
Phoebe Halliwell and Cole Turner on Charmed, although initially he was just trying to seduce her so he could kill her, He eventually turned good for a while.
In NCIS Ziva had a relationship with a crooked, alcoholic Mossad agent. It failed, spectacularly.
In Stargate SG-1, Daniel Jackson met Vala Mal Doran when she attempted to steal the Earth ship Prometheus. An undeniable attraction began soon after. In at least one timeline, they eventually got together before falling victim to a literal Reset Button.
In a Farscape connection; Aeryn Sun (also played by Claudia Black) tried to kill John Crichton (played by Ben Browder who'd go on to SG-1 as well, where the fact that he and Jackson's actor Michael Shanks resemble each other was brought up a few times). They worked out their issues and eventually married and had a child.
Nate and Sophie's pre-series relationship on Leverage...even though he remained faithful to his wife and she believes he was never really tempted.
CJ and Danny from The West Wing are a mild version of this: she is the White House press secretary, he is the chief White House correspondent from the Washington Post. Her loyalty is completely with the president and protecting him from his political enemies, and he refuses to neglect his duty to report accurately and to inform the public of as much as he can find out, two sets of interests which of course come into conflict quite frequently. They mainly have an up-and-down cycle of trying to date, pissing each other off, giving each other the cold shoulder, trying to date again, breaking up because of ethics worries, being unable to resist each other, deceiving each other again and fighting over it, ad infinitum.
A rare happy ending is implied for this couple, as CJ quits politics despite an offer from incoming president Santos, to go run a much-less-controversial charity initiative.
Jack and Juliet from LOST. They started to develop feelings for each other before Juliet's Heel-Face Turn. Then later, in the 1970's time travel sequence, Sawyer and Juliet. Although, by this time Juliet is a full Face and Sawyer's intentions are always questionable. You could also argue Kate and Sawyer considering Sawyer's Heel-Face Revolving Door.
John Connor and Cameron in The Sarah Connor Chronicles. He's the future savior of mankind, destined to save humanity from a race of machines. She is part of that race of machines, and originally programmed to assassinate him. Though reprogrammed to be one of the good guys, it doesn't always stick... Sexual tension ensues. And how.
Party Animals: Ashika, a Tory MP candidate, and Scott, a lobbyist turned campaign manager for her Labour opponent. After a lot of UST, they do fall in love and sleep together but at the end of the series she's convinced, wrongly but with good reason, that he's leaked the photos that cost her the seat.
Servalan and Avon. The blatant flirting and occasional bouts of passionate kissing move this one out of the realms of subtext, but it's still not really a relationship because neither of them trusts the other any further than they could throw a cake underwater.
Emma and Olly from The Thick of It. Well. He's working for the Secretary of State for Social Affairs and Citizenship, she's working for the shadow Dosac secretary. But then their bosses know about their relationship and his at least actively encourages it -just so Olly can leak policies to Emma, or know of hers. It also works the other way round. However, it's not clear that they actually even like each other...
While they are not the lead characters in Battlestar Galactica, the relationship of Captain Karl "Helo" Agathon and a Cylon copy of Lt. Sharon Valerii is suitably star-crossed. note The original is codenamed Boomer, and the copy eventually adopts the codename Athena. And despite the attempted gang-rape, demotions in rank, distrust, and Presidential baby-stealing, they are, as of the midpoint of season four, fairly happily married.
Until Boomer shows up and impersonates Athena.... Despite his near death in the finale, they get a happily ever after.
The trope is deconstructed when Spike and Buffy get together in Season 6 — the result is a Destructive Romance, due to Buffy's self-loathing over the relationship and Spike's failure to understand Buffy's moral qualms.
Most of Xander's love interests turn out to be demons. He even nearly married Anya, who created a universe in which Xander died twice during her first appearance.
Not just Buffy either. Faith actually does Xander after several prods about whether Buffy has (not to mention she tries to rape him when he doesn't want to have sex with her), and she wants to know what Angel was like. She later tries to get into his pants counting on him going evil because of it (in her words, she intended to stretch out that 'moment of happiness' into a long weekend) before it becomes a strong, non sexual friendship during her Heel-Face Turn. And she teases Spike over what she or Buffy could do to him, then later they discuss sex and it's hinted they did it.
And there was one episode when Oz was into that other werewolf.
On Angel, Wesley and Lilah Morgan. Angel/Eve. (Lorne made them do it!) Angel/Faith in season 4 and (arguably) Gwen Raiden.
For all the animosity between them, Firefly's Mal and Saffron do manage to show a teensy, tiny bit of affection toward one another - when they aren't Pistol-Whipping each other or leaving the other party naked to die in the middle of a desert. And don't forget, they technically aremarried.
Only if you don't count her flagrant bigamy — who hasn't she married?
Pops up in Dollhouse with the brief interaction between Bennett Halverson and Topher Brink. Both of them are hammered hard by their various Geeky Turn Ons even before they meet each other (Topher considers Bennett a supreme genius, and Bennett has a massive crush on Topher) and there's several adorable moments between them, including one where Topher ends up implying to Bennett without saying anything that he thinks she's beautiful, and has a priceless embarrassed reaction. In fact, Topher says she would have been perfect, except for the fact that she's insane and wants to brutally torture and murder Echo for leaving her to die. Kinda kills the relationship....
And yet somehow, they're back to flirting in her next appearance, until something even more drastic comes to kill their relationship.
Omen of Dark Oracle, a recurring antagonist, nursed a fairly serious crush on Cally, one of the protagonists, throughout its run. Whether he was just using her initially is up in the air, although by the end he cared enough to take a bullet for her.
Power Rangers Time Force has another one-episode version: Lucas the Blue Ranger is a ladies' man, and Nadira falls for him after she discovers some love poetry he's written. This is unfortunately one-sided, as she's Daddy's Little Villain and said Daddy Ransik is an Overprotective Dad; after Ransik puts Lucas through some Twerp Sweating he panics and starts going "Please Dump Me!" By the way, that poetry that Lucas wrote was actually for his car. They do seem to get together post-season, though, once Nadira and Ransik have both made Heel Face Turns.
In Power Rangers Ninja Storm Dustin with Marah, but she ends up betraying him after considering a Heel-Face Turn. When she and her sister bail on Lothor for real at the end of the series, she's quick to ask Cam if Dustin still has a crush on her. Cam says they can talk about once they're out of the exploding spaceship.
In Babylon 5, Vir Cotto helps Narns escape the Centauri occupation while his ditzyfiancee Lyndisty fondly remembers killing entire villages.
By series 6 of Doctor Who, the Doctor became romantically involved with a convicted murderer and psychopath raised to assassinate him. She succeeds more than once, but he keeps coming back for more. (Averted, though, in that very early on in their relationship (from her perspective) she changes allegiances completely, and her loyalty is absolutely and without question with the Doctor from there on out.)
Gary and Anna Alphas, though neither of them have any real contempt for each other, and are more close friends than anything else.
Jack Bristow and Irina Derevko on Alias. Even though she was a KGB sleeper agent who posed as his wife and constantly walked through the Heel-Face Revolving Door, they clearly wanted to debrief each other quite badly.
Complicated by the very real betrayals on Irina's part, not just the original swallow mission, but multiple subsequent betrayals of both her 'husband' and their daughter. Her attraction to Jack is clear... unfortunately, neither her love for Jack nor her daughter either of them, for that matter could overcome her addiction to Rambaldi's work.
Kono's mystery boyfriend on Hawaii Five-0 has turned out to be Adam Noshimura, the heir to Honolulu's yakuza clan. Admittedly he's trying to turn their operations legit, but he's not finished yet.
Dexter and Lila in season 2. It says something when Dexter is a serial killer and the girl he dates is darker than him.
Dexter and Hanna McKay in season 7.
Scandal: The beginning of Quinn's romantic relationship with Gideon, a cub reporter who seems on the verge of breaking the Amanda Tanner story.
An especially tragic end, as Gideon dies and Quinn is effectively framed for the murder.
In Vegas there's a definite attraction between Jack Lamb and Mia Rizzo from about the second episode, and the two end up in bed at the Christmas Episode and secretly dating after. The one is the younger brother of Sheriff Ralph Lamb and his right-hand both on the ranch and in the squadroom, and the other is a senior finances manager at a mob-run casino and the daughter of a made man.
Sam Winchester and Ruby in Supernatural. The former is a hunter of supernatural monsters, the latter a demon. She eventually seduces him while mentoring him to kill other demons, and they start a physical relationship. In a later episode their foreplay jumps straight into Hemo Erotic territory when she lets him drink her blood, to which he is addicted. When he admits it to Dean, his brother is more than squicked out. One of the few examples in the series that isn't just one-sided Foe Yay from a villain towards one of the heroes.
Sherlock and Irene Adler, who is actually Moriarty, on Elementary. She seduced Sherlock into a relationship in order to figure him out and why he kept foiling her criminal plans, but did eventually develop real feelings for him. Once she got what she wanted, Moriarty then fakes "Irene"'s death so that she can be free to pursue her plans without Sherlock's interference.
Blondie's "X Offender" is about a prostitute who falls in love with the police officer who busts her.
In the rock/metal opera project Aina: Days of Riding Doom, Syrius and Orianna fall deeply in love, despite being commanders of opposing sides in the war. And half-brother and half-sister. Not that they know it, to be fair.
Kirby Krackle's song "Then Again, Maybe Not" is sung from the point of view of a superhero who is a little tired of fighting his arch-nemesis, and suggesting that grabbing some Mexican food and flirty conversation would be a better idea.
Nobilis: Nobles have shacked up with Excrucians on grounds ranging from "screw Lord Entropy, Love Redeems" to "someone told me not to". One Running Gag in third edition is that Jenna Moran (author) and Miranda Harrell (one of the artists) have...ambiguous relationships with the Excrucians Genseric Dace and Coriander Hasp, respectively.
Sly Cooper and Carmelita Fox. He's a heroic Gentleman Thief, she's a dedicated police officer. It's kind of one-sided to start with, but she softens up in the climax of each game, then gets really angry when Sly slips away.
At least until the third game, where they actually hook up for good at the end. Sly willingly gives up his life of crime and all of his friends, saves her life, and fakes a convincing amnesia act to let her justify it. Then in the next game, it's back to business. Sort of.
The situation with Silk Fox and the player (either gender) in Jade Empire starts out looking like this, before a variety of revelations related to the Gambit Pileup point out that she is most definitely a good guy.
Alex, the only real Love Interest in The Bastard Of Kosigan series is also the brains behind one of the main villain's operation. Though, due to the story's Black and Gray Morality, she shows up much more on the grey side of the scale than the French, the Inquisition, or the witches, so perhaps she and Mordred aren't actually villains after all.
In Harvest Moon - Magical Melody you can marry your rival, Jamie, who is always the opposite gender from you. Considering that in the original Japanese, there were rival marriages much like most of the rest of the series for all the other bachelor(ettes), you and your rival are the true pairing. Sadly, however, your game ends if you marry them, and you can't even find all the magical notes.
Leon Kennedy and Ada Wong of the Resident Evil series alternate between teaming up and pointing weapons at each other. All while oozing so much Unresolved Sexual Tension into the air that it could be cut with the proverbial knife.
In Assassin's Creed, the Assassin Altair and the Templar Maria end up falling in love, despite being enemies. This is shown in Assassin's Creed II, where Desmond even has a memory of their child being conceived, and Altair's Codex contains a hand-drawn portrait of her.
Worth noting that Maria actually switched allegiances in Assassin's Creed: Bloodlines, and canonically the romance came afterwards.
Commander Shepard (Alliance) and Miranda Lawson (Cerberus) in Mass Effect 2.
All but outright stated between Aria T'Loak and Nyreen Kandros in the third game's Omega DLC. Aria is the cold-blooded ex-merc whose word is law on her Wretched Hive, Nyreen's ex-turian military and always thinks about the little people ("she oozes virtue"). It ended when they realized it couldn't work unless one of them changed, and Nyreen didn't want that to be her.
Kohaku in Tsukihime during her route. During the same route, there was a little with Akiha as well, but Shiki decided that their relationshipdidn't depend on blood. But for the main thing, it's the only way that Kohaku actually gets to have a happy ending. In the rest, she either continues bottling up her emotions (canon personality) dies or loses her memory, perhaps intentionally.
Umineko no Naku Koro ni has Battler and Beatrice, whose romantic undertones are there, but not quite strong or obvious. However, in the end, it turns out that not only are they romantically involved (in a way), but the romance between them is basically the cause of everything that happens in the series. Possibly subverted, since Beatrice is not actually the real antagonist, but a faux one (although Battler believed she was the real antagonist for most of the series)
Evil Inc..: Captain Heroic and Miss Match. There was also an affair between Commander Heroic and Flame long ago, and lately Lightning Lady and Elastic Man have developed a relationship.
Denny Levens was a retired inventions supplier for the mob. When he learned that the Hebbleskin Gang was behind some purchases, he got out of the business. His past hobbies don't make him a threat to Candi directly; but the fact that she marries a Hebbleskin deserter makes her enemies want her dead even more.
Baron Klaus Wulfenbach has canonical amorous history with Lucrezia Mongfish a.k.a. the Other. That's pretty solidly in the past, though; she's used creepily familiar terminology and physicality, but he was clearly not responding and anyway she does that to everyone.
The Baron's son Gilgamesh and main heroine Agatha Heterodyne, with the dramatic twist that though they're both noble and heroic, circumstances keep putting them on the opposite side. And it was about four (real-life, not webcomic) years between their scenes together. Damn you, Foglios!
In Casey and Andy, Jenn has been crushing on Quantum Cop for ages, and it turned out that her feelings were reciprocated (just in case their time-traveling daughter from the future wasn't proof enough..) Complicating their relationship is that he is literally The Perfect Cop, while she's an International Jewel Thief. He doesn't seem to mind much, though.
The reader doesn't find out that Jenn is a crook until nearly the end of the strip, although Quantum Cop figured it out years earlier. The author did plant clues for a really long time.
Early on in Sluggy Freelance Torg has this situation when he develops a crush on Val, who is revealed to be a vampire. Torg inevitably has to kill her.
And then there was his promise to marry Oasis...a promise he intended to keep. (One only wonders how Zoe's death will affect that...)
In Erfworld, Wanda and Jillian arguably had such a relationship at one point.
It must be said the Wanda was simply using magic to manipulate Jillian into being her unwitting servant.
Deconstructed with Durkon and Hilgya. They were attracted to each other, and seemed to be coasting towards a Relationship Upgrade, but their differences in alignment proved irreconcilable. Another problem was that Hilgya was technically still married to someone else Their breakup was considered the series' first major Tear Jerker
Elan and Therkla, though it was incompletely requited (Elan is mostly devoted to Haley).
In The Adventures of Dr. McNinja, Dr. McNinja and Hortense. They used to be dating, but broke up... then meet up again where she's trying to stop Doc from saving the world. Of course, it turns out to be Doc's parents trying to get the two back together. Later, she's revealed to be working with King Radical, but there's still some romantic tension between the two.
The Rocket of Legion of Nothing wooed Ghostwoman during WWII, when he was fighting for the US and she was a Nazi Superspy. Unsurprisingly, this was the topic of the first LoN fan-fic.
Los Hermanos, a member of the Global Guardians is having a torrid affair with Brigit, the daughter of Lord Doom via one of his copy bodies.
In Chaos Fighters II-Cyberion Strike, Etliz, a wanted criminal and Etlisk, one of the police officers tasked to catch her and her comrades go as far as an actual date after Etliz was saved from getting naked when Etlisk put a final blow which stops clothing damage on her. a subversion occurs when she pulls a Heel-Face Turn later on.
In an episode of Batman Beyond, Terry McGinnis meets and starts to fall for a girl...who turned out to be Ten of the Royal Flush Gang. As the gang is arrested, Terry asks Bruce, "this kinda thing ever happen to you?" Bruce smiles. "Let tell me you about a woman named Selina Kyle..." Eventually the girl leaves her family's gang and gets a regular job and lifestyle, unfortunately she had betrayed Terry and Batman's trust once again before going straight, and Terry wasn't interested in leaving his steady girlfriend for her. As a conciliatory note, the end of the episode reveals that her actions convinced her brother to leave the gang as well so she's not entirely alone.
Blackarachnia: I like being a bad girl. And you know something else? Somewhere deep beneath this squeaky clean armor-plating of yours, I think you like it too, hmm?
For double points, they had this relationship in the sequel series as well. but in reverse: Silverbolt's spark was in one of their foes and Blackarachnia was determined to convert him as he had converted her.
Ćon Flux and Trevor Goodchild, of course. Though which of these is the villain is debatable.
In X-Men: Evolution, Kitty/Shadowcat of the X-Men and Lance/Avalanche of the Brotherhood of Evil Mutants got together during the second season, though unlike most cases the villain in question was acting much more noble than previously, and the relationship led to a considerable amount of character development for him later.
Keeping on the X-Men theme, Wolverine and the X-Men does this with Nightcrawler and the Scarlet Witch. However the relationship between them is difficult to define. Kurt cares about her and tries to steer her on the right path, yet never openly admits he cares about her as anything more then a friend. Wanda herself does love Kurt and it's admitted as such, but its hard trying to date an X-Man when your father's ideology directly opposes theirs. Wanda throughout the first season struggles between the loyalty to her father and her crush on Kurt; in the end Nightcrawler's charm finally seeps through and she rejects her father partly because of Kurt's influence, mostly because he was willing to sacrifice other mutants to achieve his ultimate goal. Before anyone thinks this is completely out of the blue, there is actually a universe in the Marvel Multiverse where Kurt and Wanda did get together and they have a girl named Nocturne. Still, it's kind of a stretch nonetheless.
Not the biggest stretch when considers that Nightcrawler has often been portrayed as having a strange ability to attract women like flies to a bug lamp. In one of his miniseries Beast even notes that he's jealous since there both blue, furry, and look like demons yet he can't get a girl and Kurt, at the time, had three girls after him.
The Venture Bros. has murder machines extraordinaire Brock Samson and Molotov Cocktease back when they were both secret agents.
Rusty tries to invoke this with Dr Girlfriend, but she isn't interested.
Dr Girlfriend attempts to invoke this on Brock, he's not interested (He think she's a post-ops transsexual).
Dr. Orpheus also wants to get in on this trope. When lobbying for his own archenemy, he requests an attractive redhead to maximize the possibility of UST.
Spy Groove. Spy #1 finds himself falling for Sierra Nevada, who's brilliant, gorgeous and evil.
The old Sunbow G.I. Joe series had an episode with Joe computer specialist Mainframe falling in love with Dreadnok Zarana while the latter was undercover infiltrating GI Joe headquarters. In a rare example of continuity, this relationship became significant in a later episode.
In C.O.P.S., COP Sgt. Mace and cat-burglar Nightshade had a romantic relationship despite being on opposite sides of the law.
Teen Titans: Cyborg starts dating Jinx when he goes undercover at the HIVE Academy, although it's the flirtatious Kid Flash who starts Jinx down the road to her Heel-Face Turn.
El Tigre featured the titular character and Black Cuervo. The two dated twice, though they did so for their own personal reasons. Whereas Manny Rivera/El Tigre became disenchanted with her when he discovered she was just using him, Black Cuervo in turn developed a hopeless crush on him. Matters are made worse when Manny's best friend, Frida Suárez, is rivals (and not of the friendly kind) with Black Cuervo's civilian persona Zoe Aves... with whom Manny seems to get along fine. Cue Love Triangle.
As a bonus, Black Cuervo's mother and grandmother (Voltura and Lady Gobbler) have had their own failed relationships with El Tigre's dad and grandfather (White Pantera and Puma Loco) in the past. Generation Xerox played straight.
Justice League: In one episode while he's being held prisoner by the Injustice League, one of Batman's moves to disrupt their unity is to seduce Cheetah...What is it with Bruce Wayne and cats, anyway?
This plot thread was carried over to the official tie-in comic, where she faked a Heel-Face Turn in order to woo the Flash, who simply thought she had legitimately reformed. After finding out that Flash had a date with reporter Linda Park, Giganta gave up the charade and tried to kill them both.
Darkwing Duck had the hero falling for 'evil businesswoman' Morgana, though she easily Heel Face Turned for both of the schemes she was in on because she felt the same way. She even knew his secret identity by season three.
On WordGirl, kid villain Tobey is rather explicit about his crush on the titular superheroine. She continually rebuffs him, though reluctantly admits she enjoyed herself when he once tricked her into spending the day with him.
Naturally has this between Batman and Catwoman in several episodes. One even has them become a crimefighting team, having a child, retiring and finally dying together. However, it was all just a book written by Alfred.
Talia al-Ghul is depicted as a teenager in this version. Robin flirts with her in her first appearance, but she shoots him down. In her next she frees Batman from a Death Trap, and when he asks why, she kisses him. He takes it stoically. "I see."
One episode also has Jonah Hex hooking up with Lashina, depicted here as a henchwoman of Mongul and Mongal.
Young Justice has Red Arrow and Cheshire, just like the comics. After some one-sided flirting in the first season, they get married during the five-year Time Skip, only to split due to Arrow's obsession with finding the original Roy Harper. When Cheshire reveals they have a daughter, they get back together and have now reached Battle Couple status, complete with Cheshire carrying baby Lian around in a papoose while they kick ass. She loves it.
The Spectacular Spider-Man has the usual heavy flirting (and one kiss) between Spider-Man and Black Cat. However, they part on less friendly terms after she blames him for her father, who is Uncle Ben's killer, refusing to break out of jail.
Offered in TRON: Uprising. Impressed with how Beck (in his normal guise) managed to deal with an incident involving a Runaway Train, Paige suggests Beck look her up when they get back to Argon in order to "hang out", which Beck doesn't refuse. And this is on top of the Foe Yay the pair already have going on...
Variation with Vanessa Doofenshmirtz and Monty Monogram from Phineas and Ferb. It's really their dads that are on opposite sides, but they have to keep it secret anyway.
While not exactly a "hero", Professor Farnsworth of Futurama has some history with Mom, which resurfaces in a few episodes.
In Kung Fu Panda: Legends of Awesomeness One episode, Shifu's old flame Mei Ling comes to visit whom he dumped in their youth because she was a conniving thief. She tries to get back together but he refuses. finally when he does start to feel for her she uses a mystical stone to swap bodies so disguised as Shifu she would trick Po and the Furious Five into robbing a vault for her. In the end after everything is back to normal, Shifu sends her to prison. Which she escapes before arriving and runs off somewhere. The ending implies Shifu still having feelings towards for her.
Also there was an episode where Po's father feeling betrayed and unappreciated starts dating Scorpion (A recurring villain, since he doesn't pay attention or seem to even care about Po's Kung-Fu life so he knows nothing of the enemies on the show) though Scorpion was only getting close to him since he was catering a festival which she planned to poison the entire valley.
Truth In Television
Neither person was evil, but American political strategists Mary Matalin (a Republican, and quite conservative) and James Carville (a Democrat, and liberal enough) faced each other across several elections in The Eighties, culminating in the 1992 campaign (in which Carville engineered Bill Clinton's winning strategy), still regularly appear across from one another on political debate shows, and call one another arch-enemies. They not only dated, but are married (getting hitched in 1993) and the proud parents of two daughters. They understandably do not talk politics at home.
Rival NASCAR racers Danica Patrick and Ricky Stenhouse Jr. announced they were dating while both were competing for the 2013 NASCAR Rookie of the Year Award.