Robin and Starfire and also Kid Flash and Jinx on Teen Titans.
Aang and Katara in Avatar: The Last Airbender. Co-creators Mike and Bryan openly state that it is not the result of fan opinion, but a concrete element of the storyline from the get-go when they were developing it around 2003. It's not hard to believe that Aang/Katara was intended from the get-go, since there's a He Is Not My Boyfriend moment in the second episode. The two eventually become Happily Married with three children after the end of the series, right up until Aang's death prior to the beginning of The Legend of Korra.
Kim and Ron. When the series came back for a fourth and final season, the creators have repeatedly commented that they backed themselves into a corner with the trope, and had to be extremely careful not to jump the shark or gross out the ten-year-olds watching.
Dr. Drakken and Shego are hinted to become this at the end of the series, during a Last Minute Hookup.
Bonnie and Senor Senior, Jr. are not only an official couple, but also the Beta Couple, which must rankle Bonnie as the Alpha Bitch.
Danny and Sam in Danny Phantom. Really not much of a challenge, as the only other major available female characters are the proverbial Catwoman and a second example of a Romantic False Lead. Like most examples, at times, it's almost as if she's only there so that the writers can drop anything-but-subtle hints at the prospect of them "pairing up" in the last two seconds of the series.
Robin (a.ka. Nightwing) and Batgirl in Batman: The Animated Series. At least until they have a falling out over Batman, and it's implied that Barbara and Bruce became involved.
Raf and Sulfus from Angel's Friends. Their love and relationship make up much of show's drama, and even the plot centers around them.
Justice League UnlimitedGreen Lantern (John Stewart) and Hawkgirl, going through a whole era of being Star-Crossed Lovers when Hawkgirl's people invaded and she cooperated with them. Even once those issues were eventually cleared up, Stewart was in another relationship and had a hard time due to lingering feelings. Things were made even more complicated when he met his and Hawkgirl's Kid from the Future Rex/Warhawk from the Batman Beyond era. The series ends with them apart; it's been stated by Word of God they will settle for each other eventually as John didn't want to get together Because Destiny Says So. According to the Batman Beyond Unlimited comic (via multi-part short stories), Vixen is killed by Shadow Thief. John swears revenge and shaves off his goatee. Shayara decides to go with him as Adam Strange appears, telling them that their target is causing trouble on Raan. They zeta-beam there, where in the ensuing fight Stewart slays the Shadow Thief. The Guardians of Oa are less than pleased that one of their officers used their power for revenge, and Stewart is stripped of his ring and place amongst the Corps (on top of that, the Guardians decide not to let Earthlings be Lanterns for a while). After burying Vixen in Africa, a local holy man blesses Shayera and Stewart's relationship, and this eventually leads a bouncing baby bird boy. And then there's the other official Beta Couple pairs of Huntress/The Question, Green Arrow/Black Canary, and Supergirl/ Brainiac 5.
In Batman Beyond, it has the new Batman, Terry McGinnis, and his mostly-steady girlfriend Dana Tan. The JLU episode "Epilogue" confirms their official couple status by strongly implying that Terry was about to propose to Dana.
Chiro and Jinmay were pretty well set-up from Jinmay's introduction, which is amazing for something Toon Disney used to run.
Nova and SPRX-77 as well; and they had a Slap-Slap-Kiss vibe through the show's entire run, which makes it even more astonishing it ended up on Toon Disney.
Ed and Deetz from Get Ed are confirmed through episodes as liking each other that way (with on screen kisses, shock).
Codename: Kids Next Door: Numbuh 3 and Numbuh 4, and, as confirmed in the finale, Numbuh 2 and Numbuh 5. Numbuh 1 and Lizzie were an Official Couple for six seasons but broke up shortly before the series finale (and it's never told if Numbuh 1 found someone else).
Goliath and Elisa in Gargoyles, from the third episode of the series. Acknowledged between themselves in the Second Season Finale.
Beast Wars: Blackarachnia and Silverbolt; carried over into Beast Machines, where Blackarachnia redeems a brainwashed Silverbolt via The Power of Love. What made this very poetic was the fact that Silverbolt, in the preceding series Beast Wars, had been The Ace and Blackarachnia had been the Dark Action Girl (and Silverbolt had been the one to convert her to the good side), so Blackarachnia being the one to redeem Silverbolt after he had originally redeemed her in Beast Wars was a nice way to bring things full circle.
Adventures of the Galaxy Rangers: It's Zach/Eliza, Shane/Niko, and Doc/Maya. This fandom is highly unusual as it won't cross those lines for the main four. The only time it might is in flashbacks, or "missing scenes" for a couple episodes.
Gwen and Kevin in Ben 10: Alien Force. Ben and Julie were aiming at this until their breakup in Omniverse and in the end, it's Ben and Kai.
Henry and June form KaBlam! start out being friends, but with June having a crush on Henry (and usually shows this by being a total brat towards him). The so-called "series finale" ended with her kissing him, and in season four (at least until after "A Nut in Every Bite!"), the duo have stopped fighting and became closer than ever before (cue "awwwwww"s).
Cuddles and Giggles in Happy Tree Friends. An odd example, as she has been shown flirting with (or even dating) other characters even after the couple was established. Then again, this is Happy Tree Friends, where characters frequently die horribly only to be fine in the next episode...
Fry and Leela in Futurama. Amy and Kif end up as the Beta Couple. Played with in some episodes, when their relationship wasn't defined, yet was official nonetheless- the fact that they have feelings for each other was always evident, and they even went out on dates. In an episode where they break up, even Fry was surprised that they were dating.
Superboy and M'gann, as of episode 11. Though they've broken up during the five year time-skip and now M'gann and La'gaan are a couple. Also Wally and Artemis, as of episode 26. And played straight, they have been together for five years during the time-skip.
Mal Duncan and Karen Beecher, who have been together even longer than Conner and M'gann.
Eventually in episode 44, M'gann breaks up with La'gann and reconciles with Conner in the series finale.
Stan Marsh and Wendy Testaburger, but they broke in the Season 7 episode "Raisins" only to get back together in the Season 11 finale "The List". However, Wendy breaks up with Stan again in Season 20's "Skank Hunt", but they appear to have gotten back together again in the Licensed GameSouth Park: The Fractured but Whole .
Craig Tucker and Tweek Tweak as of the episode "Tweek x Craig". While the nature of the episode's plot led to debate for a while about whether or not the relationship was genuine or if they were just close friends pretending to date for the sake of the town, the episode "Put it Down" removed as good as all doubt with scenes such as Craig referring to Tweek as "babe" and "honey" even when it is very unlikely anybody they know is present. Word of God confirmed this later on Twitter, and it's also proven in the Licensed GameSouth Park: The Fractured but Whole through their interactions, their character sheets, and their combined Ultimate Attack, "Eros Eruption", if you help them get back together during a sidequest.
My Little Pony: Friendship Is Magic: Despite avoiding romance for the most part, at least insofar as the main characters are concerned, the show does include a number of canonical, stable couples.
The the most focused on relationship is that between Twilight's brother Shining Armor and Princess Cadance, whose wedding took place in a major two-parter episode and who have since had a daughter.
There are also the main characters' parents — such as Twilight's parents, Night Light and Twilight Velvet, Pinkie's parents, Igneous Rock and Cloudy Quartz or Applejack's parents, Bright Macintosh and Buttercup (neé Pear Butter) — whose relationships have also had some focus.
Other official couples include Mr. and Mrs. Cake (who have also had kids), Cranky Doodle Donkey and Matilda (whose wedding was the focus of another episode), Applejack's brother Big Macintosh and Sugar Belle, and Pinkie's sister Maud Pie and Mud Briar.
Fluttershy's parents, Rarity's parents, and Rainbow Dash's parents are also seen. All of them are Happily Married.
Big Macintosh eventually becomes an official couple with Sugar Belle, one of the ponies from Starlight Glimmer's old village. One episode is spent trying to woo her, and another is an elongated Third-Act Misunderstanding, but the two of them have been together ever since they first hooked up.
A Meaningful Background Event in "The Big Mac Question" has Lyra Heartstrings proposing to Bon Bon and there's even an image of their wedding in a newspaper in the Season Finale. Given the sheer amount of Ship Tease between these two dating back as far as Season 5, to the point that "best friends" was obviously a tongue-in-cheek euphemism for "lovers", literally nobody was even remotely surprised.
The series finale "The Last Problem" gives us Pinkie Pie and Cheese Sandwich.
Finn and Flame Princess were aiming at this until their breakup in "Frost and Fire".
Finn and Huntress Wizard in the final season.
As of the series finale, Princess Bubblegum and Marceline.
Jonny Quest: The 80's animated series had two tv movies (Jonny's Golden Quest and Jonny Quest vs. The Cyber Insects) both of which featured Race's daughter Jessie. She and Jonny appear to be about 10 to 12 years old. She kisses him in both movies. Also, Race Bannon and Jezebel Jade.
Mordecai and Margaret until "Steak Me Amadeus", because Margaret has been accepted into her dream college and has to turn down a possible relationship with Mordecai despite her feelings for him. Since "Real Date", it's Mordecai and C.J. There is also Muscle Man and Starla, and Hi-Five Ghost and Celia. As of "Dumped at the Altar", there is Rigby and Eileen as well.
Now that the grand finale has aired and given the audience a look into the future, there is also Benson and Pam, and Mordecai and a previously-unseen bat woman.
Ruby and Sapphire, the two Gems that make up Garnet, as confirmed by one of the storyboard artists.
As of the Steven Universe: Future finale, Steven and Connie are officially a couple with at least vague intentions of marriage in mind.
Fred and Daphne in the various incarnations of Scooby-Doo. A favorite fan theory/joke among older audiences is that the reason Fred was always suggesting that he and Daphne pair off when the gang split up for investigations was so that the two of them could sneak off to make out.
Egon and Janine in The Real Ghostbusters. Janine acted more like a case of Hopeless Suitor towards Egon, yet Egon does shows jealously over Janine's suitors in some episodes and mutual attraction (albeit very restrained in the case of Egon). They became official couple up until the sixth season. In the Sequel SeriesExtreme Ghostbusters they are presented as a mature couple living together.
In Star vs. the Forces of Evil after "Bon Bon The Birthday Clown", Marco and Jackie. However, this is ultimately subverted, as it soon becomes apparent that Star has a crush on Marco. Jackie ends up breaking up with Marco after she realizes that he also has feelings for Star. It takes another year for Star and Marco to realize it, with their Relationship Upgrade and Official Kiss coming in the late season 4 episode "Here to Help".