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The Great Mouse Detective: Given it's a movie based on Sherlock Holmes, it was inevitable, but the relationship between Basil and Ratigan, how the two are so obssessed with one another and how they drive each other crazy, is really something else.
There's some squicky subtext between Coraline and the Other Mother, from a strictly Freudian sense.
The book the film was based on actually had rather strong undertones of parental rape from the Mother.
Rafael and Nigel in Rio. There's also a bit between Nigel and Jewel. "Pretty bird," anyone?
Pitch towards Jack Frost in Rise of the Guardians After spending the first half of the film ignoring and demeaning Jack, Pitch goes to great lengths to tear Jack away from the other Guardians and join his side.
Kung Fu Panda 2 has a brief bit of one-sided Foe Yay between Lord Shen and Tigress. Towards the end, when the Furious Five are tied up and helpless before Po rescues them, Shen leans in very close to her and whispers in her ear. If they were humans rather than anthropomorphic animals, this would probably be as much I Have You Now, My Pretty as you could get away with in a children's film.
Near the end of The Princess and the Frog, Dr. Facilier offers to make Tiana's dreams come true in exchange for his talisman. He shows her illusions of her restaurant while circling her and making his offer in a VERY seductive tone.
Facilier practically seduced Naveen into making the deal.
Film - Live Action
The Western 3:10 to Yuma was chock full of Foe Yay between the captured criminal Ben Wade and the man hired to bring him in, Dan Evan. At one point, Evan and Wade are alone in a hotel room and Wade looks up at the ceiling, wondering how many brides had taken in the same view. (Funny what you notice if you spend long enough online.) But that's not the worst part...
The 1964 film Becket starring Richard Burton and Peter O'Toole is a textbook example. Thomas Becket and King Henry II of England are the best of friends...until Henry gets the bright idea to make Becket the Archbishop of Canterbury, which means Becket is now conscience-bound to oppose his king. As a result of their estrangement, Henry becomes unhinged and ultimately has Becket murdered.
Henry (to Becket): I would have gone to war with all of England's might behind me, and even against England's interests, to defend you, Thomas. I would have given away my life, laughingly, for you. Only I loved you, and you didn't love me. That's the difference.
According to author Gore Vidal, who cowrote the screenplay for the epic Ben Hur, he and director William Wyler persuaded Stephen Boyd, the actor playing the villain Messala, to portray him as though he and Ben Hur had been lovers as youths, and thus his hatred for the hero would be motivated by sexual and romantic rejection as much as by ideology. Vidal states, however, that he and Wyler did not tell this to Charlton Heston, the actor playing Ben Hur.
Black Widow (1987). There's definite lesbian subtext between serial killer Catherine and the female Justice agent pursuing her, most notably in a scene where one is practising mouth-to-mouth resuscitation on the other: "You're not taking this personally, are you?"
Child's Play: Chucky and Andy. May have started when Chucky tells his former voodoo teacher before killing him:
There's also the fact that in the second film he bound and gagged Andy to a bed, and he laid on top of him in order to perform the soul transferring.
A pretty perfect example in the 1970 Sci-Fi thriller Colossus The Forbin Project between Forbin and his creation Colosuss. It starts becoming blatant towards the middle of the film with Colossus insisting that cameras be set up throughout every single one of Forbin's rooms to monitor him at all times, with no exceptions, except for a few hours four days a week which Forbin insists he needs for man/woman sex (AKA time to plot against Colossus). Colossus comes across as a little jealous and probing, and there are plenty of scenes of him... I mean... it... zooming in on Forbin and seriously checking him out after he gets out of the shower, and after he undresses in front of Colossus.
Colossus: In time you will come to regard me not only with respect and awe, but with love.
Dr. Forbin: Never!
Arnold Schwarzenegger's character John Matrix and the antagonist Bennett in Commando, best summed up in this wonderful piece of dialogue:
Matrix: I'll be back. Bennett: I'll be waiting for you, John.
Not to mention:
Matrix: Put the knife in me and look me in the eye and see what's going on in there when you turn it. Don't deprive yourself of some pleasure... come on, Bennett, let's party!
Bennett: I DON'T NEED THE GIRL! I DON'T NEED NO GUN!I'M GONNA KILL YOU NOW!
Constantine has one-sided Foe Yay from Balthazar and Lucifer towards Constantine. Hell wants him bad.
Lucifer leans in after he appears, tries to lick Constantine's cheek and a few other places. Then after trying to stick his tongue in, nibbles on his ear. He also helps Constantine light his smoke after playing around with it.
Balthazar (to Constantine): "Word is your on your way down, fresh meat. Finger-licking good." Balthazar sucks on his fingertips.
Balthazar (to Constantine, as John's being choked): "Don't fight it, Johnny-boy, enjoy it."
Lucifer: "Your the only one I'd come up here to collect myself."
Constantine: "So I've heard."
Lucifer (to Constantine): "I've got a whole theme-park full of red delights just for you, John."
Basically the plot of D.E.B.S., which is centred around a lesbian love story between one of a team of Charlie's Angels-type heroines and the Big Bad. In fact the short film on which it is based has the villain having to think up all these nefarious plans simply so the two of them can get together for some quick sex without attracting suspicion.
Death to Smoochy: Rainbow Randolph's obsession with Sheldon (Smoochy) sure looks like this at times, like when he's in disguise driving him to the set-up Nazi rally, he starts insulting himself to try and prove Sheldon hates him, and he calls himself a "pillow biter" among other things. Later, he accuses Sheldon of being gay, saying "You should have seen the way he was eying me in the car". Sheldon even says Randolph "Might have some problems with sexual identity". And then there's the end: Smoochy and a post-Heel-Face Turn Rainbow Randolph ice skating together while Jackie Wilson's "Higher And Higher" plays.
The Big Bad of Fright Night, played by Chris "Prince Humperdink" Sarandon, is one of the most homoerotically-charged vampires in cinema history. There's plenty of Ho Yay between the master vampire and his "special friend" (not to mention the pastel pink knitwear) and Foe Yay galore between Sarandon and the protagonist, Brewster. The most in-your-face scene, though, is between Sarandon and Brewster's best friend Evil Ed, when he's literally seducing Ed to the dark side:
"Hello, Edward. You don't have to be afraid of me. I know what it's like being different. Only they won't pick on you anymore... or beat you up. I'll see to that. All you have to do is take my hand."
The remake takes this up a notch; just watch when Ed's being turned and try to say it doesn't look sexualized.
There's also the sequel to Fright Night, where Jerry's sister Regine is plotting to turn Charlie into a vampire so she could torture him for eternity. "Torture" may be subjective here, considering she kissed him before biting him the first time, danced with him, and nuzzled him while he was bathing. His roommate, who was also turned, even mentions how "she's not going to stay mad forever."
Fawcett and Soledad from GBF are always at each other's throats and by the end, you just wanna see them kiss, especially since neither has a love interest
Gilda: Johnny Farrell and Ballin Mundson. They even have a toast to a partnership without women with Ballin Mundson's cane right between them.
The Good The Bad And The Ugly. Blondie does spend an awful lot of time tying Tuco up and dumping him in places for him to start mouthing off like a jilted girlfriend. It doesn't help the comic implied the hanging scheme was initially Tuco's idea, which makes the movie look less like a Masochism Tango and more like a mutually fulfilling breathplay S&M game...
All over the place in Captain de Boeldieu's scenes with Captain von Rauffenstein in The Grand Illusion. Had that nurse not interrupted, they surely would have started making out during the hospital scene.
Draco/Harry (their rivalry) and Voldemort/Harry (that scene where he grabs Harry's face in his hand and gets close to his face) in the Harry Potter films. For the record Tom Felton claims to ship Harry/Draco, but he might be joking/playing the fan-service.
Snape/Harry, though it's just personal hatred rather than actually being enemies. Snape does like invading Harry's personal space when he attempts to discipline him, and in Order of the Phoenix he drags him by the hand down to the dungeons and then spends several scenes trying to penetrate Harry's mind. Either increased or decreased considering that Snape loves Lily Potter.
Between Jamie and Judy from the movie In the Loop. Jamie to Judy: "I'm quite aroused by the idea of giving you a long... hard... disciplinary hearing."
Followed by a Crowning Moment of Awesome for Judy, when she actually manages to shut Jamie up by coolly remarking that she would quite enjoy the "big... fat... compensation payment" she would receive as a result.
Judy: I'd love you to give me one, Jamie...
IT has the scene where Adult Ben thinks he's kissing Beverly when it turns out to be It in drag, who then shouts "Kiss me, fat boy!"
Jesus Christ Superstar. Like all good gay love stories, it ends in tragedy. Some would contend that Jesus/Judas was the whole point of Superstar in the first place. Have you listened to some of Judas' lyrics?
Elle in Kill Bill towards the Bride. She hates the Bride, but also feels a deep sense of respect for her and is enraged when she is apparently killed in an ignominious and disgraceful manner by Budd.
There is also her relationship with Bill who was a former lover. They still obviously have a lot of attraction toward one another and don't even hide it while trying to kill one another.
Labyrinth makes it blatantly obvious that Jareth has some sort of attraction to Sarah, but nothing is explicitly stated. It's especially evident in the Novelization when there was an attempted kiss scene.
In Legion, Gabriel, the badass archangel who has absolutely no qualms about killing a newborn baby (or all of humanity for that matter) is nearly brought to tears at the thought of having to harm his rival Michael, who lovingly caresses Gabriel's cheek and tells him "It's enough".
Whatever is going on between Zod and Jor-El in Man of Steel.
In the live-action He-Man movie Masters of the Universe, Skeletor takes He-Man as his "slave" by threatening his friends. He strips him to even less clothing, then has him tortured with a sort of laser-like whip while watching with almost aroused glee. To make it worse, it actually looks like He-Man is leaning his butt into the whip as if he enjoys it.
In The Matrix, Neo/Smith have something going on, what with both of them going inside each other.
It is also quite heavy on Smith's end as seen in much of his dialogue to Neo. In Reloaded, Smith says to Neo both: "I watched you die, Mr. Anderson, with a certain satisfaction I might add."
Later on: "Still using all the muscles, but, the one that matters." Implying that Smith knows a bit about how much Neo's 'other muscles' are put to use.
Then near the beginning of the final fight in Revolutions, Smith starts off by saying: "Mr. Anderson, welcome back, we missed you." Smith has no stated reason for saying this implying that he really does miss Neo.
A little bit later, Neo says: "It ends tonight." to which Smith replies: "I know it does." Making it sound like Neo and Smith were having an affair behind Trinity's back, instead of fighting like they should have been.
Also in the first movie, is onesided Cypher/Neo when Cypher istrying to kill everyone, just before he tries to kill Neo he says to Trinity: "Look into his (Neo's) eyes, those big, pretty eyes."
Merry Christmas, Mr. Lawrence: Major Jack Celliers (played by David Bowie) and Captain Yonoi (played by Japanese rock star Ryuichi Sakamoto). The Foe Yay is entirely intended - Celliers has had "no romantic interludes of any real importance" and Yonoi watches him sleep when he's in solitary confinement.
My Super Ex-Girlfriend: The titular ex-girlfriend, despite being willing to use her superpowers to pretty much attempt to kill her ex-boyfriend, she's eager to take him back, until it turns out that he's trying to neutralise her powers.
Perhaps more fittingly, the archnemesis is her old high school best friend. They were on their first date when the origin story happened and he's obsessed about her to the extent of becoming a supervillain just to get her attention. It ends in one of the rare happy endings for Foe Yay, when he admits to loving her and they become a couple. He also switches sides, since he was only a supervillain to get attention from a superhero.
There's more than a hint of one-sided Foe Yay in Onmyoji. The bad guy Doson murmurs and smiles at Seimei whenever he's done something dastardly, and commits suicide while saying that he'll be watching him. And during the final battle, he asks Seimei to rule the world with him while stroking his face and throat and clutching at his clothes. Seimei (who hangs out with pretty lady shikigami) isn't impressed by the offer.
In Dead Man's Chest Beckett, while holding the brand Jack has on his wrist, says that he and Jack have left their marks on one another. When Will inquires as to what mark Jack left on him an extremely uncomfortable look passes over Beckett's face. He doesn't answer.
The Prestige. Borden and Angier spend the entire movie being obsessed with each other, at the sacrifice of their signifigant others.
In The Quick and the Dead, Big Bad John Herod (Gene Hackman) invites Ellen (Sharon Stone) over for a romantic candlelit dinner and offers to make her his mistress if she'll drop out of the dueling contest. Later, as he's about to fight Cort (Russell Crowe), he leans in really close and says, "I've always wanted to fight you, Cort. Ever since I first laid eyes on you. It was just this itch I had to scratch." "Fighting," eh? Is That What They're Calling It Now?
Razor Blade Smile is a film about two ancient vampires battling their way down the centuries. When the heroine finally has her sword at the Big Bad's throat they make out and then start it all again, it's a game to keep them from dying of boredom.
James Hunt and Niki Lauda in Rush. They spend the whole film sniping and calling each other childish nicknames. But when a journalist is vile to Lauda, Hunt beats the living crap out of him. The final scene is also full of it, notably when Lauda says to Hunt, "I need you busting my balls." Granted, he's talking about racing, but still...
Saw has Hoffman and Jill. When he finally found her in Saw 3D, he leaned in so close to her that it looked like he was going to lick her neck.
Spartacus has so much Ho Yay between Spartacus and Antoninus, along with Crassus and Antoninus, but Foe Yay was shown between Crassus and Spartacus.
In The Sorcerer's Apprentice, Horvath calls Dave 'sweetheart' in one scene. Whilst pinning him up against a wall and putting his cane against his mouth to silence him.
The Green Goblin/Spider-Man Foe Yay from the first Spider-Man film. I mean, what with the Goblin completely ignoring Spiderman's personal space, paralyzing him and catching/carrying him bridal style to the top of a building where he chats with him about getting him to join his side. He almost seductively whispers for him to "Wake up..." and says he's an "amazing creature" and that "you and I are Not So Different". The whole time he's talking to him, he's crouching in front of a paralyzed Spidey and getting in his face. Then, the Goblin says breathlessly that compared to everyone else "we're exceptional", grabs Spidey's face tightly in his hand, turns it toward him and threatens "I could squash you like a bug right now but I'm offering you a choice. Join me. Imagine what we could accomplish what we could create..." Of course, Spiderman ends up refusing the offer and the Goblin takes it about as well as you'd expect, by pretty much acting like a jilted lover and spending the majority of his time threatening Spiderman and his loved ones, kidnapping Mary Jane and taunting Spiderman with a Sadistic Choice involving Mary Jane's life or the lives of a bunch of children, and brutally beating up Spiderman with the serious intent to kill him.
Spidey's comment to J. Jonah Jameson, telling him to be quiet because "Mommy and Daddy are talking", didn't help matters either.
Harry and Peter have this too before it goes back to Ho Yay.
Jabba/Han, especially in the Special Edition, and of course Jabba/Leia, what with forcing her to dress in the (in)famous metal bikini. In the Expanded Universe Jabba is considered a pervert by other Hutts for being attracted to humanoids.
Palpatine goes on and on about how Luke will call him "master", that he belongs to him, and that he will take Vader's place at his side. "You, like your father, are now... mine."
Speaking of Palpatine, he was getting pretty cozy with Anakin in Revenge of the Sith while trying to bring him to the dark side. Obi-Wan outright says that Anakin was "seduced by the dark side".
The RotSnovelization, based on the original screenplay and approved by Lucas himself, has bucketloads of No Yay between Anakin and Palpatine. The book establishes that Padme, Palpatine, and Obi-Wan are the most important people in Anakin's life, so Palpatine deliberately sabotages Anakin's relationship with the other two in order to have Anakin all to himself, going so far as to imply Padme and Obi-Wan are having an affair.
The novelization and post-ROTS EU take this Up to Eleven. Vader is obsessed with Obi-Wan to the point of keeping his lightsaber and cloak in his resort off the Death Star following Obi-Wan's death. Also, lightsaber/stunt coordinator Nick Gilliard said he choreographed the Episode III lightsaber fight "like a fight between spouses" since Obi-Wan doesn't want to kill Anakin but "wear him down until he breaks...at which point he can give him a cuddle."
Bruno and Guy from Strangers on a Train. Despite the censorship of the day, Bruno has a clear Stalker with a Crush vibe towards Guy. And one gets the impression Guy doesn't want Bruno to leave him alone quite as much as he says:
(paraphrased) Guy: Get out of here and leave me alone!
In the remake of The Taking of Pelham One Two Three, Ryder has a ridiculous amount of one-sided Foe Yay with Walter Garber. He demands to speak only with Garber for the whole movie and keeps getting more and more obsessed with Garber's life. Ryder spills his guts to Garber over and over and even admits in his death scene that Garber is his hero. It culminates in this hilariously out-of-nowhere line:
Ryder: He sounds sexy. He would've been my bitch in prison!
A little Loki/Sif if you look at their scenes a certain way.
The Avengers is brimming with this. Aside from the usual Loki/Thor (including-but-not-limited-to intimate face touching), one can make an argument for Loki/Tony, Loki/Clint, and Loki/Natasha. Heck, even some of the hero/hero ships in the film can be classified as Foe Yay (Steve/Tony, anyone?).
Jason Statham got no end of ribbing from the film crew on the second The Transporter movie for the "Kiss of Life" he performs on a thug in order to survive crashing into deep water. There's also that fight scene of him fending off a ton of Mooks shirtless and covered in motor oil...
Van Helsing: Dracula shows interest in making Anna his bride, and a lot of his dialogue and actions towards Van Helsing is almost flirtatious especially considering Van Helsing is the one who originally killed him.
Dracula's bride Aleera also seems very interested in Anna, calling her "my love" and making claims like "I know what lurks in your lusting heart."
Harry Tasker and Juno Skinner in True Lies. While in his spy persona, he seduces her with a tango while dodging detection from the bad guys, before either of them knew who the other really was. When they both learn of each other's identities, there is an amount of one-sided Foe Yay from Juno towards Harry, including alleging that they had a affair and kissing him in front of his wife Helen to hurt her.