Perry the Platypus and Dr. Doofenshmirtz of Phineas and Ferb practically embody this trope. At the very least they're the epitome of the Friendly Enemy, treating their adversity as a job more than any actual effort to harm one another. Then there's the episode where Doofenshmirtz acquires a new nemesis which is presented as him having an affair, culminating with them on a relationship talk show together. "My nema-nema, oooooh my nema-nema-nema..."
Slade's obsession with Robin is rather predatory. Hot-blooded Robin, of course, swiftly becomes just as obsessed with Slade.
Pretty much all of the "Apprentice" episodes. Slade holds Robin's arms behind his back while saying "I monitored your vital signs during the mission. Elevated heart rate, adrenaline, endorphins. You won't admit it, but at some level...you enjoyed stealing for me. It was a thrill, wasn't it?". Slade watches a video of Robin beating up the rest of the Titans and says that it's "thrilling." He even rewinds the tape a couple times. Later on he pretty much manhandles Robin to the ground, getting really close to his face, angry that the only thing he cares about are his "worthless, little friends!" He then goes on to say "If the Titans are so distracting, maybe I should just get rid of them." Robin admits defeat with "Don't. I'll do whatever you say." And Slade's reply? "Good boy. And from now on, I'd like you to call me master."
And in "Haunted" we get Slade beating Robin to a pulp, telling him "Alone again Robin? As long as I'm around. You're never alone" and during the climax (no pun intended) it sounds like he's raping Robin who begs him to stop and pulls his face close to his own while telling him "I am the thing that keeps you up at night. The evil that haunts every dark corner of your mind."
Afterwards, Slade transfers all of his Foe Yay tendencies towards Terra, with constant threats and demands that she do everything he says, and more sexually suggestive dialogue you can shake a stick at. Given that Slade had sex with Terra in the original comics, this is almost certainly intentional.
Rare heterosexual (presumably) example: Red X flirts with Starfire at one point.
Raven falling in love with Malchior, who lived in a book in the episode "Spellbound". However he turned out to be a Mailer Daemon, who then proceeded to trick her into releasing him from the book. While Raven was heartbroken, she did get revenge during a final fight and put him back in the book using the techniques that he taught her.
Jinx and Kid Flash end up together after an entire episode of fighting each other.
The beginning of the episode "The Beast Within" where the team is fighting a arrogant buffed up character named Adonis has Raven attempting to hold him in place with her powers but he easily breaks her hold, and tackles her to the ground where he pins her for a moment; complete with him purring "You're feisty" and grinning at her in a perverted manner while she struggles against his hold.
Terra, Raven, and their mud wrestling fight in Aftershock pt1.
Jinx's flirtatious(?) remarks to Beast Boy: "Here kitty kitty. What's the matter? Afraid of a little bad luck?"
Brother Blood and Cyborg, as displayed by his obsession over defeating and bending Cyborg's will to resist his mind control.
Speaking of Cyborg, he flirted with Jinx to the point of taking her out during his time undercover.
Zim and Dib, who are obsessed with each other to unhealthy levels even for people trying to kill each other, basing their entire lives around the other and never missing an opportunity to try and prove themselves the better of the two, even when frequently forced into reluctant alliances. It's rather disturbing, but also quite sad, as they are literally the only people in each others' lives who care about the other at all.
"Dark Harvest" has this bizarre line from Dib:
"You see, Gaz? To defeat my enemy, first I must study my enemy, then become my enemy, then move in with my enemy, then wear my enemy's clothes, then-"
In "Vindicated" it's revealed that Dib goes through Zim's trash once a week or so. Also in "Bolognius Maximus":
They display severe co-dependence in the un-aired episode "Mopiness of Doom", in which Dib "retiring" to follow "real science" like his father results in him becoming bored and listless, while Zim, no longer having an enemy to fight, becomes depressed and unmotivated.
Tak was technically Zim's girlfriend for a while (although she did it to humiliate him and he did it For Science!), and Dib showed signs of having a crush on her.
In the first episode, having just met Zim, Dib decides the most appropriate course of action is to handcuff him. With handcuffs that, in his words, render aliens "completely helpless". Handcuffs that he was carrying with him for the slight possibility that he might encounter an alien. He then chases him around with the handcuffs.
Transformers Prime gets most of its Foe Yay from Airachnid, a Decepticon with a spider-theme. She's rivals with Action Girl Arcee and is hellbent on killing Arcee's human friend Jack as revenge for his outsmarting her and destroying her ship. The way that she strokes her victims wit her claws before moving in for the kill does NOT help.
Joker awaiting Batman to show up and break his little midnight jewelry store robbery in "The Man Who Killed Batman", looking frustrated as if his date hadn't shown up.
Joker: There's a certain rhythm to these things. I cause trouble, Batman shows up. We have some laughs and the whole thing starts all over again!
Batman Beyond: Terry gets his fair share of uncomfortable moments it's his Rogues Gallery. Several of his enemies go through odd fixations with him, and special mention goes to the time when Inque makes out with him in order to keep him from warning Bruce Wayne to not come rescue him via their com link.
Joker: Oh, an entire wing [of the Batcave] pour moi? I knew you cared!
Batman also got some villainesses after him, kissing him when they get the chance. Catwoman for one. And Talia, daughter of Ra's al Ghul. Poison Ivy, though her kiss was to use her Drugged Lipstick and part seduction. Another villainness Cheetah (though Batman was purposely seducing her and the power of Kevin Conroy's voice probably did its work). Harley Quinn by far is the luckiest, getting to snagtwo kisses from the much stunned Dark Knight.
Lex Luthor in Superman: The Animated Series: In episode five he's having a 'join me' moment from at least a meter closer than necessary, not to mention his sadistic smirk makes him look quite aware they're about two centimeters apart from kissing.
Both Cartman and Kyle spend a large amount of time thinking up ways to get back at each other, usually due to Cartman doing something morally questionable and Kyle trying to stop him. The subplot of a three-part-special consisted of Cartman trying to force Kyle into sucking his balls, and travelled across the country to get him to do it. At one point he even wanted to film it. The episode ended with Cartman actually imagining him doing it, complete with calling him a 'dirty girl'.
He said (in the expanded version at least) he did it to humiliate Kyle, not for any actual sexual pleasure. Whether or not he can be believed is unknown, especially given his other borderline-homosexual tendencies.
"Tonsil Trouble", where Cartman gets HIV from a mishap while taking his tonsils out, and in turn infects Kyle as revenge for laughing at the irony; the two must travel crosscountry together to find the cure, and Kyle will frequently tell people that it was Cartman's fault that he has HIV only to be met with many, many gay jokes (they're even called "Lovers" near the end of the episode).
In "Le Petit Tourette" Cartman begins faking Tourettes and Kyle does everything in his power to stop Cartman from appearing on Dateline NBC, but initially and unknowingly ends up saving Cartman, whom had actually lost control over what he says. The episode ends with a relieved Cartman hugging Kyle and exclaiming "You DO care!" before skipping off.
Cartman risked life and limb to save his best enemy Kyle from the center of the Smug Storm, just so he could continue to spar with him. Kyle returns the favor in "It's a Jersey Thing" and Cartman notes, "Deep down inside, you're a monster. But you're my little monster!"
Cartman's life is empty without Kyle to rip on, while, in "Cartmanland", Cartman's misery is what gives Kyle reason to live and believe in God.
It's assumed during the events of "Cartman Finds Love", that Cartman/Kyle became canon in-universe, at least as far as Cartman (who himself started the rumor of their being together)/the rest of the school is concerned. Kyle himself is more distressed/enraged that Cartman started the rumor in the first place.
Craig and Tweek in "Tweek vs. Craig", where they beat each other to a pulp. Almost naked. In winter.
Remember that one episode, back in Season 4, when Wendy and Cartman, who are usually enemies, pair up for a debate and subsequently fall so hard in Foe Yay that Wendy dreams about Cartman riding into a mountain meadow, shirtless, on a white horse?
Danny and Vlad. Vlad's first appearance alone has him creeping into Danny's room just watching the boy struggle in his sleep, then there's Danny's foot massage request in "Torrent of Terror", not to mention the multiple attempts Vlad has done to try and lure Danny into the dark side which when taken in a different context, it sounds almost seductive. And of course "Eye for an Eye" which is a treasure trove of subtext quotes ("I'm rubbing your nose in this mess you made, Daniel, doesn't it smell yummy?" and "You forgot to take your supplements, have a dose of vitamin-ME!" for example). That episode also has them seeing each other naked. Then there's the fact Vlad made a prepubescent female clone of him... whom he only planned to use to perfect a male clone. The Slade-Robin similarities don't exactly help, either. Given Vlad's obsession with Danny's mother and desire to make Danny his son, Freud would definitely have something Oedipal related to say about it.
Dark Danny and Danny have one-sided Foe-Yay, with Dark Danny being the one generating it. At one point, he forces a Time Medallion inside Danny's body while Danny screams in pain.
Valerie and Danny in their secret identities also get a bit of Foe-Yay, which is especially egregrious considering they dated for a while as their normal selves.
Ben and his Evil Counterpart Kevin in Ben 10 get very close before Ben realises what a sociopath Kevin is, and even afterwards Ben often tries to help him and is rather sad at what he's become (as opposed to all his other enemies, who he usually just beats down no questions asked). In the Time SkippedSequel Series, Ben 10: Alien Force, the writers seem to be having a lot of fun writing Ben/Kevin subtext to complete the triangle with Gwen, though (un)fortunately Kevin since performed a Heel-Face Turn, making it standard Ho Yay.
"Alone Together", where Ben and a Highbreed named Reinrassic III are trapped on a desert planet and forced to team up if they want to survive. In the end, "Reiny" (the Highbreed; guess who gave him the nickname?) decides to stay behind after declaring he has been "contaminated" by "Ben-Ben" and thus, does not want to spread the contamination for the rest of his species.
In the Season 2 finale, "War of the Worlds", Reiny returns to convince the rest of the Highbreed Council that Ben's genetic fusion of the Highbreeds with various other alien DNA was actually a blessing that would allow their dying race to persist. He's in turn made the new Highbreed Supreme and ends the war by calling a truce and shaking Ben's hand as a sigh of respect.
From Race Against Time, the live-action movie, Eon has a persistent and disturbing tendency to grab Ben by the arms and shove him against a nearby wall while muttering some at times very suspect dialogue.
What makes this worse is that Eon intends to turn Ben into a younger version of himself using the Omnitrix so that his more youthful incarnation can use the Hands of Armageddon to start a Chronian invasion of Earth. He briefly succeeds in this endeavor. Race Against Time is regulated to "alternate timeline" status in Ultimate Alien, but there it turns out that Eon is Ben and he's going around various other timelines enslaving all of the other Bens and turning them into his flunkies. Yeesh.
Gwen and her own Evil Counterpart, Charmcaster, also have this. When Charmcaster first sees Gwen in her debut appearance in Alien Force, she has this to say: "I've waited five years to say this... I love what you've done with your hair."
And speaking of Omniverse, there is Princess Looma of the House of Red Wind, although she's not explicitly evil; she just happens to hail from a particularly war-oriented society. In the interim between the original series and its sequels, it's revealed that Kevin fought and defeated Looma in exchange for an engine for his car, but thanks to Tetramand customs, this also made Kevin Looma's fiance, set to be married in three years' time. Not wanting to be burdened by such a commitment, he sets up the entirety of "Many Happy Returns" as a Batman-Gambit to pawn off Looma on Ben. It works. Despite Ben's ever-growing Chick Magnet credentials throughout the franchise, he is decidedly vexed and dismayed about this predicament, and with good reason: he's now engaged—against his consent—to a Proud Warrior Race Gal who is rather clingy.
Trevor Goodchild in Ĉon Flux is explicitly depicted as Aeon's lover and submissive as well as being her nemesis. He's so obsessed with her that, in one episode, he's shown with a whole harem of women who look similar to her. They also have a tendency to have sex in the middle of battle.
Bugs Bunny and Elmer Fudd from Looney Tunes. Heck, the two end up running off to get married at the end of the cartoon "Bugs Bonnets", thanks to the influence of a set of personality-altering hats.
Not to mention Bugs and Daffy Duck. In this Kids' WB! promo, Jeff Bennett describes them as "two big stars who just LOVE each other", and the cartoon "Beanstalk Bunny" has Daffy actually kiss Bugs when he reveals his escape plan.
The Monarch's obsession with Dr. Venture in The Venture Bros. is dripping with one-sided Foe Yay. Anyone who doesn't see this should watch "Mid-Life Chrysalis" again.
This was made even more blatant when the Monarch was caught screwing GUARDO, a robot with Dr. Venture's face.
Before this he waxed ecstatic about how sweet his loathing for Venture was and how it lent purpose to his life, and how hollow his existence seems now that he's forced to stay away from his One True Hate. And let's not forget his enraged accusations of abandonment before murdering Dr. Dugong and his fantasy conversation with Venture while flipping through the Guild facebook.
Scott and Lance probably top everyone with their Foe Yay. Lance just seemed to always get under Scott's skin and make him nuts. Lance's big Heel-Face Turn episode, "Joyride", felt more like a Lance/Scott episode than a Lance/Kitty one thanks to their tension. And screenshots like this just speak for itself.◊
Even before Evo, look at the previous cartoon. There were a significant number of these moments, occasionally bordering on regular Ho Yay, between Magneto and Xavier, especially in the series finale - somewhat Hilarious in Hindsight seeing as several years on, Magneto would be played in the live-action films by Ian McKellen, who is both gay and quite open about it.
The episode "Snow Bound" had Timmy and Vicky Locked in a Freezer (well, a cave, but the effect is the same), leading to a surprisingly touching bonding moment, a near-complete mental breakdown on Vicky's part, and hugging. And early in that episode, Timmy's dad explains that women often say the opposite of what they mean - for instance, Wanda calls Cosmo a moron when she means "I love you." A simple joke, or the writer implying/foreshadowing that Vicky is Tsundere?
In another episode, Timmy wishes to have the body of a sixteen-year-old, and Vicky instantly becomes massively infatuated with the "Norwegian supermodel", enough to want to marry him. Foe-Yay-tastic!
Vicky seems awfully fond of putting Timmy in dresses. Who can forget that maid's dress from "Homewrecker"?
In one episode Timmy tells Vicky that he can't sleep because he has dreams about her giant butt. Sure, he was just provoking her to test a new wish, but still...
The time that Timmy's attempt to serenade Tootie, in order to get her back to loving him instead of his brother (It Makes Sense in Context), got heard by Vicky instead.
Ruby-Spears' Mega Man: Suspicious dialogue aside, there's not much to suggest this between Mega Man and Proto Man—until "Bro Bots." Proto Man pretends to "go straight" (*snicker*) and join his little brother—nothing wrong with that. Until the park scene, anyway—blatant hand-holding on Mega's part, plus his confession that "I've always wanted a real brother relationship with you." The last fight in the episode has the two brothers fighting on a ridiculously small space over a gigantic pool of acid. This would be perfectly innocent if Protoman wasn't very obviously straddling Mega Man, and if Mega didn't wrap his legs around his older brother's waist—and if their almost falling into the acid didn't bring their bodies even closer together. "Real brother relationship", indeed.
Parodied in Freakazoid!! with the Lobe's obsession with the titular character.
It's hard to believe this wasn't at least partially intentional. It's hard to think of a Mozenrath episode that doesn't either turn Aladdin into a Distressed Dude or have the two of them end up wrestling on the floor at some point.
Mozenrath: I'm going to put my essence...into your body.
Heck, it started as early as Mozenrath's very first episode.
Mozenrath: Look, the important thing is, we found each other.
Mozenrath has this with Jasmine, too. He seems to be rather fond of her, and he strokes her chin when the gang gets captured sneaking into his city. She also has a very impish smile on her lips when she tries to use her whip on him a bit earlier.
He also refers to her as a "cutie" at several points, and tells Aladdin to "give the Princess my regards". Xerxes then starts making kissing noises as Mozenrath smiles.
Jasmine: Please, Mozenrath! Leave my father alone! I'll give you anything!
Mozenrath:(gives her a suggestive look)
Kim Possible and her Evil Counterpart Shego. Two women who jump at each other for close combat whenever they meet, stopping only to exchange witty banter and fashion snark? When the show returned for a fourth season with Kim and Ron as the Official Couple, the producers ramped up the Foe Yay by having Shego save Kim from an alien Amazon because "I am not going have this she-thing defeat Kimmie! That's my job!" and even turn good and immediately become close friends with her for a while... The fact that this pairing is only marginally less popular than the Official Couple in the fanbase probably says the most about how noticable it is.
You've got to contextualize it: One of Robotnik's captives was rescued by Sonic in order to find his High School Sweetheart. However, this girl was also Robotnik's unrequited crush at the time, and Robotnik's motivation in locking him up was to prevent them from reuniting. Eventually, they do, and to distract Robotnik, Sonic dresses in drag as the crush and weds him. (This would be potholed to Attractive Bent-Gender, but that doesn't even cover it). Still, it doesn't excuse his kissing Robotnik five times, not to mention licking him after splattering him with cake...
Sonic seduces Robotnik again in "Sonic is Running". He slips on a dress and says to presidential candidate Robotnik, "Oh, Robotnik. You men in power are so...powerful! Isn't there somewhere we could be alone?" Robotnik is all too willing to comply, simply because his "wife" for the election is a robot.
There's also the business of Scratch trying to seduce Sonic's ancestor in "Robotnik's Pyramid Scheme".
Wes Weasley's debut episode has Robotnik making his point about who he's trying to catch by pointing to a photo of Sonic, which for some reason is signed "To Robotnik. Love, Sonic."
Piper/Cyclonis is hilariously obvious. When Cyclonis disguises herself to infiltrate the Storm Hawks and becomes friends with Piper in the process, Cyclonis actually grows to like Piper while Piper is genuinely hurt at the betrayal. As Piper got more in touch with her Dark Magical Girl side Cyclonis starts popping up in Piper's dreams, practically seducing her as she tries to bring her to The Dark Side. Despite all the cliches around The Hero and the Evil Overlord, it's not Aerrow but Piper who becomes Cyclonis' primary enemy and the only one with the power to defeat her.
Aerrow's famous "But I don't want to see the Dark Ace!" line.
Tom and Jerry... what? Don't tell me you didn't see it. Because you did.
Indeed. There's even one episode in which Jerry actually kisses Tom. On the mouth.
In one of the earliest episodes of Tom And Jerry, which was of course a Christmas one, Jerry stops Tom from chasing him by holding up a mistletoe and making a cute smoochy face at him. Tom then blushes and turns away shyly, only to have Jerry kick him in the rear.
Not to mention that whenever one of them (usually Tom) finds a girl, the other seems to get really jealous that they stop paying attention to them (most blatant when Jerry sees Tom with a new girl after failing to get a reaction out of Tom, and his evil angel appears saying "You and him got a sweet thing going on! You gonna let some dame get in the way of that?" before helping Jerry to break them up).
And then there's the end of Heavenly Puss when Tom (happy that he's still alive and he just had a bad dream) hugs and kisses a confused Jerry.
Gargoyles: If you want enemies who "because of their defined roles, the two characters must fight, but (at least one of them) would subconsciously rather be doing something else," look no further than David Xanatos and Goliath. It's clear from the get-go that Xanatos wanted the gargoyle clan leader to be his friend, not his enemy. Xanatos seemed genuinely disappointed when he realized Goliath couldn't be convinced to work peacefully with him, doesn't even try to hide how much he enjoys fighting either with him or against him in combat, and then there's this thing involving them both being "fathers" of this clone who shares the best and worst traits of both of them...
Thailog could be seen as the ultimate nadir of a spiral of obsession. Xanatos' every move screams Stalker with a Crush...from moving an entire castle across the Atlantic, to building his Steel Clan robots in Goliath's likeness at the end of the Five-Episode Pilot, to modelling his Powered Armor after him...Even the (male) mutates are all built like crosses between Goliath and furries. Indeed, it's hard not to get buckets of Foe Yay out of Xanatos' actions throughout his villainous career...and when Goliath agrees to move back in with him, the cloning, robot-building, etc. all stops...like a Stalker who's finally got the object of his desire?
Goliath/Demona, Brooklyn/Demona, and Macbeth/Demona are all canon.
Sailor Moon did her magical costume change to fight the villain... who then proceeded to get a hard-on, which made everything awkward, so they both decided to call off the fight. Later the villain reported to Queen Beryl and her yelling at him turned him on again. Later, Queen Beryl obsessed over a photograph of Sailor Moon and she got hard also.
Samurai Jack needs to be mentioned... Aku has turned into a woman and tries to seduce Jack. Slowly, developing a full relationship with him. Repeatedly. Likely done to make Jack suffer as much as possible when he finally learns the truth but still he doesn't have to do personally.
ReBoot has Bob and Hexadecimal. It isn't exactly one-sided either, as Hex is able to make even Bob's canon love interest jealous, and he's never as hard on her as he is with Megabyte. Their relationship almost becomes canon after her Heel-Face Turn, and she kisses him before her Heroic Sacrifice.
Possibly parodied in Futurama where, in "Normal Combat", LizardMan and Purple Ninja kiss in the Normal Combat equivalent of a fatality.
In one episode of Legion of Super-Heroes, Superman is fighting a villain his age, Drax, who comes from the Phantom Zone. Toward the end of the episode, as the fight draws to its close, Drax literally pins Superman to the ground and leans down, smiling, just inches away from Superman's face. It looks very... suggestive, to say the least.
Chris Rowley didn't help matters, either by posting his speculations about Her Majesty's "private" life on the fan list, or by commenting her Evil Gloating over his unconscious body in "Psychocrypt" had "S&M vibes."
Homer and Ned Flanders, come on! It's the Trope Namer for Stupid Sexy Flanders, for God's sake! Homer has also kissed and hugged Ned, filmed him naked in the shower, and Ned puts up with every Jerkass thing Homer does.
As Told by Ginger: Blake Gripling towards Carl Foutley. Deep down he wants to be Carl's best friend, but as Carl turns him down time after time, he tries to best the youngest Foutley whenever he can. Blake also has a dislike for Hoodsey, Carl's best friend. To a lesser extent, there's also Miranda and Ginger.
Blossom and Mojo Jojo. Sure, he is a Card-Carrying Villain and she's The Cape, but when one digs deeper, they're Not So Different. In fact the only real difference seems to be that Blossom wants to be admired and Mojo feared. They can be ruthless, they like to lord it over others, and they are at the same page intellectually. Mojo is the person Blossom goes running to for help when confronted by an alien menace the girls can't defeat in "Forced Kin", suggesting that she respects him; and Mojo considers the girls as his only real obstacle to world domination, also suggesting a considerable deal of respect. Mojo is obsessed with the girls, and Blossom has outright stated she prefers brains over looks - while being dressed up as Mojo Jojo in a costume party! That last one goes beyond subtext into outright Getting Crap Past the Radar category...
The Powerpuff Girls being 'Nice' to the Rowdyruff Boys.
Brick's... um... 'flirting' with the girls.
Brick: You can't stop a good thing, babe.
Also... Embracing him also while giving him some 'sugar', as Blossom would say.
Bubbles Oh! Oh! I want the blond! I think he's cute!
Gorillaz: Murdoc has hints with both his male bandmates, though it's stronger with 2D, who actually once announced "Awww, I love you, Murdoc!" in an interview and puts up with everything Murdoc does to him (which has included stealing both his girlfriends and his internal organs).
This could be due to 2D's naivety, who always falls in Murdoc's traps, because he still obeys him, in spite of the fact that Murdoc has kidnapped him, keeps him locked and constantly abuses him, especially in Phase 3. Even in the early years, Murdoc was beating him and treated him like a Butt Monkey.
The Mighty Ducks sees Dragaunus grabbing and manhandling Wildwing while cloaked, along with all the rolling and grabbing that goes on during their fights, trying to convince Wildwing his friend is never coming back. Extra points for Dragaunus being voiced by Tim Curry.
One episode of Donkey Kong Country had King K. Rool stealing a love potion and using it to turn Candy and later DK into his willing slaves. It's exactly what it sounds like.
Generator Rex: Rex is very committed to taking Van Kleiss down, while Van Kleiss generally acts quite friendly towards him and says things like "you're very important to me." Van Kleiss claims this is because Rex is important to his master plan. Uh huh. Sure.
There's also Rex and Breach. One episode had Breach kidnap Rex to put in her dollhouse while referring to Rex as her "new favorite" and "shiny thing." It's decidedly one-sided on Breach's part, as Rex finds the whole situation rather creepy. It's also a rather unique case in that the episode with most of the Foe Yay never showed the two directly interacting.
Duncan and Noah. Seriously, who grabs someone's lip as a threat?
Alejandro and Noah, previously just regular Ho Yay.
Alejandro and Heather. It's actually a main plot point.
Alejandro: Heather has a way of making my focus slip, like a too small Speedo. This race is my redemption. As long as I travel alone, she can't distract me with her clever words, or her distrustful eyes, or the way she tucks her hair behind those cute little earlobes. (slaps himself) Focus!
Heather has a lot of this with her enemies- Gwen and Leshawna in particular, as well as Lindsay after Season 1.
Gwen and Courtney's rivalry may be shaping up to be this.
Clone High has Scudsworth totally fixated on John Stamos.
Kyle and Sigmund from Fanboy and Chum Chum. To summarize, the two used to attend the same school for wizards, before Kyle was kicked out for turning one of his teachers into... er... raspberry flan, and was moved to a regular school. In "Sigmund the Sorcerer", Sigmund visits the town he now lives in to give a magic show, and is invited (or, more truthfully, invites himself) to Kyle's house for dinner. Kyle is acting extremely soft and non-snarky throughout the entire episode, and he is evidently envious of Sigmund's more advanced skills in wizardry. Sigmund, on the other hand, refers to Kyle with pure mockery and arrogance. When Sigmund says "You know, Kyle, I must say, that I am very impressed with you", Kyle chokes on his drink slightly and asks hopefully "Really?", clearly indicating his respect for Sigmund and concern in his opinion. Blatant Foe Yay aside, at one point Kyle even submissively offers to spoon-feed Sigmund after he expresses his discontent at the cutlery being non-self-moving.
"And after this is over, I'll have four sweet, sweet words for you." "Ohh, 'I love King Julien'?" "Ye-NO! 'I told you so'!"
This is a really odd example, especially for the age it was aimed at, but in the Care Bears II movie, Dark Heart and the human Christie seem to have feelings for each other. At least it seems like he hits on her a lot. Him being an evil...magician? demon? hateful thing with no origin? and her being a human who makes a deal with him, the foe part comes in when she helps the care bears escape and is (nearly) killed in the process and he begs the care bears to save her. And then he turns into a boy with blue eyes. And then they're all friends at the end and go swimming together.
Dark Heart: (after Christie saved his life) You saved me. Why? Christie: Good or bad, you're still a person... or whatever you are. Dark Heart: If you knew what was good for you...you would have left me.
"Magic Duel" has The Great And Powerful Trixie outright stating that defeating Twilight Sparkle became her highest priority after she (indirectly) humiliated her, and after her defeat Twilight focuses all of her attention into defeating Trixie in a re-match, complete with the gem "I can't stop thinking about Trixie!".
Discord spends "The Return of Harmony" creeping on all of the mane six, especially Twilight, what with frequently invading her personal space, picking her up and hugging her, and at one point he strokes her face. And while he exchanges maybe half a dozen lines with Celestiaall of them are said in a playful, flirtatious manner, including "Did you miss me, Celestia? I missed you...".
This is how the changelings operate, impersonating a loved one then draining the love they're provided by their unsuspecting enemy. Relatedly, much speculation arose around Shining Armor and Chrysalis, what with the latter impersonating Cadance for who knows how long.
Ahuizotl: The ring, Daring Do! Give it to me! Daring Do: Now, Ahuizotl, you know I love you, but I can't give you the ring till I've properly proposed.
For some, Courage the Cowardly Dog and Katz. In a few episodes he gives Courage a fighting chance and often plays sports with him. In his words, he says, "Care for a sport of game before dying old chap?"
The Red Guy and Super Cow (a.k.a Cow) in Cow and Chicken. He tried to play with her in an episode called "Can Cow Come Out to Play?"
Marceline and Princess Bubblegum seem to be enemies - at the very least they're highly antagonistic to each other - but the episode "What Was Missing" drops anvil-sized hints that they were previously a lot closer and still yearn for that relationship again.
The Ice King is way too obsessed with being Finn's "friend", even if he wasn't a creepy old pervert and Finn wasn't a thirteen-year-old boy. Entire episodes have been created just so everyone can confirm once more that Ice King is a stalker, sexual predator and enjoys the company of his most hated enemy far too much.
The Gender Flip episode, which turned out to be a fanfiction by the Ice King about a girl version of Finn being in love with him.
In said episode, Fionna and the Ice Queen went on a date together.
Cheshire and Red Arrow from Young Justice have flirted; in Teen Titans Go!! they fell in love in a Valentine's Day comic. It's a Mythology Gag, because in the comics they did have a relationship and a daughter.
As of "Salvage," said relationship and daughter are officially canon
Totally Spies!: Sometimes is directed towards Clover and Alex with all the I Have You Now, My Pretty situations they get into. Also, in the episode "Wild Style" after Clover gets turned into a Cat Girl the villainess of the episode calls her a "pretty kitty".
Peter Griffin and Carter. While trying to get him wealthy again, they portray characters from Dawsons Creek. Peter played the girl, and he tried to kiss Carter. While Carter grudgingly tries to hold him back.
Meg and Connie. The latter is one of the main sources of the former's abuse, but there have been a few occasions of affection. For example, in "Dial Meg for Murder" a toughened Meg knocks Connie unconscious and gives her a deep tongue kiss, and Meg shows some affection for her in "Stew-Roids".
Duck Dodgers: Dodgers and the Martian Commander. The episode Enemy Yours goes out of its way to make them act like disgruntled lovers, what with Dodgers panicking when he finds out that Marvin has other archenemies and Marvin making excuses to his current archenemy as if Dodgers is some Psycho Ex-Girlfriend who is trying to sabotage their current relationship.
Canon example: Dodgers and the Martian Queen. Seriously, the woman veers between wanting to destroy him and wanting to marry him. However, it seems a bit one-sided, as when confronted with the Queen's feelings, Dodgers usually either exploits them to his own advantage, or outright rebuffs them. If he manages to remember that they were ever engaged in the first place.
When they really did get married, he had no problem with it, until Marvin tricked him into leaving her. When Dodgers found out he was duped, he seemed pretty mad.
Even after I.Q. High reveals to her that Dodgers is an idiot she still finds herself strangely attracted to him.
Spider-Man: You are the bossiest damsel in distress I have ever rescued.
Also as usual between Spidey and Venom.
Spider-Man and the Green Goblin
Spider-Man: Ooh, nice banter. Aim still needs work. Goblin: Practice makes perfect. Spider-Man: Keep telling yourself that.
Taken to its logical conclusion in The Critic when Jay Sherman is seduced by a beautiful woman at his sister's debutante ball. Jay eventually learns that the woman plays Humphrey the Hippo on television, an Expy of Barney that Jay hates. She explains that she became attracted to him after he criticized her while she was making a public appearance as Humphrey.
The Mask had this moment with Pretorius in "The Bride of Pretorius": "Mask, your powers are bizarre, unpredictable and beyond the realms of science ... and if you were a woman I would marry you." The Mask is suitably squicked.
Dr. Claw sometimes falls into this territory in his extreme hatred for Inspector Gadget, what with his constantly spying on him (even at home!) with his hidden cameras and replying to things Gadget says as though somehow the inspector could hear him through the monitor, randomly having pictures of Gadget on his person and Gadget dolls, and always saying things like "I've got you right where I want you" and "I'll get you next time, Gadget! Next time!"
Futurama sometimes has Zoidberg showing a little too much interest in Bender.
Mike and Kane of Motorcity have Foe Yay out the wazoo. Mike is deeply, personally hurt that Kane lied to him and used his fake affability to try and make Mike his loyal enforcer. Kane however genuinely did feel affection for Mike, going on and on about how Mike betrayed him - him personally - and never misses a chance to berate Mike for it, which is peculiar given that lots of other people have defected from Kane Co. who he doesn't care about at all.
Superjail has the Warden and the Mistress, two rivaling prison wardens who began bickering over their superiority as soon as they met. The end of "Ladies' Night" even culminated in them sleeping together, though not by choice as the Mistress was bitten by a Spanish fly. Although lustful due to its influence, she's shown to quickly be disgusted and horrified at the reminder of sleeping with him, while the Warden smugly considers her humiliation a victory for himself. In her second major appearance in the series, she was revealed to have taken over the Warden's prison while he was away and demotes him and Jared to being inmates, presumably as extended revenge for her humiliation and defeat.
The Warden and Lord Stingray also have a deep rivalry shown in the series, stemming from the Warden imprisoning Stingray after he attempted to take the jail for himself. The Warden initially seemed VERY enamored with the other guy and kept doing all he could to impress, unaware of what being a supervillain actually entails. If anything, it seems the rivalry is more active on Stingray's part, with his obsession with wanting to one-up the Warden.