Alvin and the Chipmunks: Alvin and Brittany are forever fighting, but clearly have the hots for each other.
Ben 10: Omniverse: Ben has this in spades with his "former" crush Kai Green (the granddaughter of an old friend of Grandpa Max). They do nothing but bicker yet the attraction is so blatant that the Forever Knights assumed that Kai was Ben's girlfriend, while Rook called their incessant arguing "romantic bantering."
Crystal Kane and Ace Mc Cloud from Centurions, Crystal tries to be as professional as she can be, but is often unnerved by Ace's braggadocios and flyboy attitude, when the two finally kissed at the conclusion of 'The Better Half', Ace had to spoil the moment by making it a more public display for his teammates.
Mung and Truffles from Chowder love each other, but they do spend much of the time arguing or, in the case of the latter, snarking at each other, with Truffles insulting his cooking. Justified since they're married.
Numbuh 4 and Numbuh 3 in Codename: Kids Next Door. Numbuh 4 is a tough-as-nails macho guy who hates all the cute and girly things that Numbuh 3 loves, causing them to fight whenever he insults her tastes. They got a thing for each other, but Numbuh 4 won't admit it.
Gargoyles: According to Greg Weisman himself, Brooklyn and his mate Katana's relationship—at least early on—was described as a gargoyle version of Much Ado About Nothing's Beatrice and Benedick. He first described it as being like Sam and Diane's relationship. No one got it. So then he compared to Beatrice and Benedick, which everyone got. That should tell you something about the show's fans.
Gravity Falls: In an attempt to help Robbie get out of his funk after his breakup with Wendy (and to prove her matchmaking skills), Mabel attempts to set him up with Tambry, a girl just as gloomy as he is. When the two end up on a blind date, they immediately start arguing (having known each other for years), and claim that it will never happen. However, they still stick around for the food, and Robbie calls her "Tambers", a nickname she had previously told someone else earlier in the episode not to call her. There was clearly something there, and they probably would've ended up together eventually, even without Mabel's meddling to speed things up.
The video game of the show, Gravity Falls: Legend of the Gnome Gemulets, shows that Pacifica and Dipper seem to be falling into this trope as well. When Mabel points out that the two hugged at Northwest Manor, they both immediately deny it ever happening and act disgusted towards one another.
Arnold and Helga. Although Arnold is definitely not a jerk, Helga's constant bullying has made him hostile towards her (or at least as much as he can be) and Helga is one of the greatest Tsunderes you will ever see.
Arnold's paternal grandfather, Phil, admits in one episode to having a similar with a girl in his youth—the girl in question is ultimately revealed to be Gertie, Arnold's paternal grandmother.
KaBlam!: Henry and June. June makes a habit out of constantly teasing Henry, much to his irritation, but she still loves him very much. She was actually very depressed when Henry left her in one episode.
The relationship between Kaeloo and her friend Mr. Cat can sometimes go into this territory, as they fight with each other about trivial things half the time.
The relationship between Stumpy and Pretty becomes this as the series progresses. They're always beating each other up and insulting each other, but both of them have also expressed a desire to kiss each other in different episodes.
Kick and Kendall in Kick Buttowski: Suburban Daredevil. One second they'll be at each other's throats, the next they're doing some activity that'll most likely end with either both giving a Longing Look or having a Twice Shy moment before it gets interrupted.
Link and Zelda in The Legend of Zelda (1989) animated series. Link usually tries to get a kiss from Zelda in some way, usually after saving her from danger, though these advances are either rejected by her or, whenever she accepts them, their moment is ruined in some way or another, whether it be something happening that angers Zelda into not wanting to kiss Link anymore or Ganon and his minions attacking them in that moment. Zelda does actually love Link as shown in "The Missing Link", though she doesn't admit to it and usually covers it up by making fun of him. This relationship was the Trope Namer for Well, Excuse Me, Princess!
Moonbeam City: Dazzle Novak and Pizzaz Miller, despite a yearly sex-filled weekend during the annual "Cop Con" police event, involving multiplerounds of love-making. They both pretend that the attraction, passion, and genuine affection they display for each other at "Cop Con" is just a "foolish, drunken, sexually-charged mistake" even though they both show their true feelings when she saves him from an assassin's bullet (then immediately have passionate sex on the auditorium stage, under a covered table). They also make love twice after the event, including within the shrubbery at a "Routes 6 and 9" bus stop.
In The Simpsons, Bart often has the kid version of this going on with his classmates and frequent tormentors Sherri and Terri Mackleberry. According to Homer, he has a crush on one of them, and at least one of them is said to have a crush on him (they're impossible to tell apart). In their Establishing Character Moment, he's been threatened with a punishment if he makes one more sound and they deliberately get him in trouble by simultaneously kissing him on the cheek, causing himto scream.
Cartman and Wendy in South Park. Cartman's early crush may have already been diminished by the time she beat the shit out of him in season twelve.
Discussed in "Envoys" when Ensign Mariner tells Ensign Tendi that she likes to start an argument with a cute lieutenant because she finds it attractive when an "uptight hunk is all wound up."
Between Ensign Mariner and Commander Ransom in "Temporal Edict." After an intense argument, he stabs her foot with a crystal battle blade, and she finds him hot while he fights shirtless during his Trial by Combat. She later throws an object at him in Sickbay and threatens to kill him, and he admits that it was kind of hot.
Mariner also has this dynamic with Andorian crewmate, Jennifer Sh'reyan, who initially seems to just be her Sitcom Arch-Nemesis. Though it is also heavily downplayed as the relationship gets much less belligerent before they actually start dating, after Jennifer saves Mariner from floating off into space.
Star Wars: The Clone Wars provides Obi-Wan Kenobi with a "past" in the form of Duchess Satine. They play it out pretty much like Benedick and BeatriceIn SPACE. Then there's the byplay between Kenobi and Asajj Ventress. One wonders what the two will do when trapped in an escape pod together.
Heather and Alejandro in World Tour. Both have met their manipulative match and sparks are flying.
Stephanie and Ryan from the Spin-OffTotal Drama Presents: The Ridonculous Race are this when their break-up is ending and they're close to reigniting their relationship. They still yell, snark and belittle each other but a few compliments and double entendres slip in as well, signifying this.
Musa and Riven in Winx Club. She's crushing on him early in season 1, but he doesn't reciprocate and instead dates Darcy. During season 2 they start to get closer, especially at the Red Fountain Concert and in the Wildlands. Riven eventually gains feelings for Musa, and they start dating at the end of season 2, and Riven is seriously injured by Dark Bloom specifically because he went Taking the Bullet for her. They have a lot of arguments however and broke up once when Riven thought Musa was getting too close to Jason Queen in season 4. Riven regrets breaking up and manages to win her back over, but their relationship remained unstable, and they ultimately break up for good in Season 6.
In Young Justice (2010), Artemis and Kid Flash get off on the wrong foot, due to Kid Flash resenting her for replacing Red Arrow/Speedy. The more they argue, the higher the sexual tension between them gets. Lampshaded in "Bereft" by Robin, who tells them to Get a Room!.