The season three episode "What Was Missing" caused an explosion in the popularity of Bubblegum/Marceline, and from there it grew until it almost dominated the whole fandom, with by far the largest chunk of fanart and fanfiction devoted to them (and their genderbent versions, for that matter). Combined with the large amount of Ship Tease within the show and comics, plus Word of Gay, most AT fans effectively treated the pairing as canon. Then they had The Big Damn Kiss in the finale, properly rekindling their relationship.
Another fan preferred couple would be the genderbent versions of Marceline and Bubblegum, Marshall Lee/Gumball.
Finn is often paired with his genderbent counterpart, Fionna. Though just as many authors and artists depict them as either Just Friends or long-lost twins, usually the latter.
Fionna and Marshall Lee already had plenty of support even without him saying or doing anything. But then "Bad Little Boy" rocketed the ship to the top and it hasn't looked back.
Tommy/Kimi and Chuckie/Angelica are both fairly popular in the All Grown Up! fandom, the former because it is suggested that she might have a crush on him in one episode and the latter because of the surprising amount of chemistry they have as an Odd Couple.
The Amazing World of Gumball: Among the show's fandom, the Gumball and Carrie ship remains popular even after Gumball and his love interest, Penny, became an official couple in season 3 while Carrie got together with Darwin. Interestingly, Ben, the creator of the show, finds the fans' pairing amusing. This is referenced in "The Shippening", in which Sarahs fan fiction comes to life: when the brothers come across an adult Gumball and Carrie with a baby, Darwin yells at Gumball for stealing Carrie from him.
The Zuko/Katara (aka "Zutara") fanbase is legendary, considerably outstripping both Official Couples Kataang (Katara/Aang) and Maiko (Mai/Zuko) put together. The "Ember Island Players" episode lampshaded this tendency heavily with a play that put Zuko and Katara together and having her refer to Aang, repeatedly, as "like a little brother". Not to mention, that this couple provides the literal cover image for this trope. It was a long-standing rumor that this pairing was one of the bigger arguments the show's creators and the head writer had, with the latter wanting to explore this relationship while the former steadfastly kept for Kataang, which became the Official Couple. Said writer would confirm in a Reddit AMA that the interview in which he allegedly said this never happened, only adding to the "Fan-Preferred" aspect of the ship. Even later material like the comics depicting the official pairing hasn't done much to dent Zutara, with many even calling out Shipping Bed Death; it's to the extent that the fanbase still exists for The Legend of Korra, with these fans operating under the idea that Katara and Zuko began a relationship in their old age following the deaths of their respective partners.
Despite Sokka having a canon girlfriend in Suki, more people ship him with Toph (who canonically has a Precocious Crush on him).
In the Batman Beyond fandom, the majority of the fans go for Terry with his best friend Max or one-time girlfriend Melanie. Few actually pair him with his canon girlfriend Dana Tan, as she's the least developed character of the three. In the Season One DVD Behind the Scenes featurette, it is discovered that Alan Burnett wanted to write an episode where Terry and Max ended up together, but Bruce Timm refused, as he'd originally intended the episode to have Terry and Dana stay together, and Terry ends up getting hitched to Dana in the future as shown in the JLU episode "Epilogue."
The original series had Ben and his cousin Gwen, due to what became a majorwriting fumble. They were originally supposed to be friends/classmates before the writers changed their minds and made them cousins to justify always having Gwen tag along with Ben and his grandfather on their adventures. This resulted in their constant bickering being perceived by fans as Belligerent Sexual Tension. Even after being officially paired off with other characters, Ben/Gwen remained the fandom's OTP, resulting in loads of H-art and fan made videos of them together.
Ben 10: Alien Force: For a period of them on FF.net, four of the five most favourited romance stories are Ben/Kevin.
Ben 10: Omniverse introduced several possible love interests for Ben before settling with Kai, a character from the original series. Unfortunately for Kai, she had two things going against her: 1) the shipping was heavily focused in the final arc, with the writers introducing Spanner to actively force the pairing, and 2) Looma Redwind and Esther were very popular since their debut, while Kai was polarizing since her debut thanks to her treating Ben like a literal dog. Esther/Ben itself is the more popular het ship for Ben.
Until well into 1990, Chip 'n Dale: Rescue Rangers' preferred shipping was Dale/Gadget, pairing the only girl on the team with the fun-loving goofball rather than with the bossy workaholic. But then came "Good Times, Bat Times" and brought Foxglove with it. She and Dale looked so cute together in what came closest to a happy relationship for a Ranger in the entire show that Dale was out of the Love Triangle for many many Rangerphiles. Fan Fic and Fan-Art keep shipping the two, and the Boom! Comics support this ship as closely to Canon as possible.
This did make way for Chip/Gadget, but while they do have a whole lot of supporters, they're the reason for a case of Broken Base: Despite Tammy's crush on Chip ("Adventures in Squirrelsitting") and Gadget's potential crush on Sparky ("Does Pavlov Ring a Bell?"), the question isn't with whom to ship Chip and/or Gadget. It's rather whether or not to ship Chip and Gadget. Among the fans, there are the Pros who support this ship and make it the second Fan-Preferred Couple, there are the Antis who oppose it, whether or not they have an alternative, and then there are the Neutrals who keep themselves outside of the debate.
Codename: Kids Next Door: Just about any non-canonical pairing involving Nigel Uno is more popular than his canon relationship with Lizzie — though the most popular seems to be Nigel/Rachel (1/362), with Nigel/Abigail (1/5) as the second most popular. The former gained a large lead following the show's finale, which revealed Numbuh 5 married Numbuh 2.
It's surprisingly common for fans of Courage the Cowardly Dog to ship Courage with Shirley the Medium, the most likely reasons being because of the fact that both characters are the only prominent characters on the show who are anthropomorphic dogs and because of how handy it could be for Courage to have someone as experienced in dealing with monsters and other paranormal creatures as Shirley around in the event that the Bagges were attacked by another supernatural menace and Courage for some reason didn't have time to consult his computer on what to do.
The Critic has Jay and Alice, which is one of the reasons why the web series wasn't well received. Considering how much trouble Jay went through in season 2 to be with Alice (especially the next to last ep), you can't blame their reaction at seeing Jay trying to woo another girl.
In Danger Mouse, Despite the occasional hint towards Jeopardy Mouse and Danger Mouse, and much teasing from the show concerning DM and chief science advisor Professor Squawkencluck, fans have gravitated to the idea of Penfold having a relationship with Squawk. Other fans gravitated to the thought of Penfold and Danger Mouse together also. The show eventually began catering to all of these preferred couples in selected episodes and now it's a question of which one will emerge triumphant at the end of it all. In the early days of the series, Danger Mouse was also paired in fanfics with the often calamity prone and endearingly polite Danger Moth. Jeopardy is often paired up with Count Duckula due to a throwaway script-editing gag in one episode where Duckula tried to write Jeopardy dating him into the story. The recent festive musical episode ''Melted' also raised the possibility of Danger Mouse having feelings for Dawn, the daughter of arch-nemesis Crumhorn, but this in itself is a complicated subject considering Dawn is underage.
Much of the fandom dislikes Daria/Tom and would have preferred that Daria's one-sided crush on Trent eventually been noticed and requited.
For some bizarre reason Jane also gets paired up with Mr. D of all people fairly often.
On DC Super Hero Girls , the most common pairings are Wonder Woman/Harley Quinn due to their opposites attract vibe, Supergirl/Batgirl due to how they supported each since the former moved to Super Hero High, Harley/Ivy and Lady Shiva/Big Barda for the same reasons as WW/Harley as the well as the latter's bonding in Hero Of The Year, and Flash/Frost due to how they're almost always paired up in background scenes.
Quite a few fans of Downtown would rather have Alex become a couple with his best friend Jen than with his crush Serena due to him and Jen having better chemistry and knowing each other better.
Despite the writers saying there would be a strict No Hugging, No Kissing rule when it came to Webby and the boys, that didn't stop fans quickly pairing her with Dewey due to her spending the most time with him out of the triplets, working closely with him on solving the mystery of his mother's backstory, and their shared thirst for adventure.
El Tigre has El Tigre and Black Cuervo, which was only helped by the show confirming that the men in the former's family are destined to end up in a (short-lived) relationship with the women in the latter's at some point during their lives. It was so popular that 'Tigre + Cuervo Forever', a catch phrase for the following, became the title of an episode. Meanwhile, Frida gets paired with either Dr. Chipotle Jr. or Sergio a lot. Frida/Django is quite popular, too. Word of God later confirmed that all these pairings end up happening during high school and college.
Brian/Stewie from Family Guy gets a lot of love, given how blatant Stewie's affection for Brian is and the amount of episodes centered around the two and their interactions. The episode Brian and Stewie is especially well-received by fans of Brewie.
Meg/Neil for some. In "8 Simple Rules of Buying My Teenage Daughter" and "Once Bitten", she was actually happy to go out with him.
Although Fillmore! was created as a No Hugging, No Kissing series, Fillmore/Ingrid have a fanbase of a rather impressive size. The shippers have a lot to base off of, since their buddy-cop conversations can often be taken as a subtle Double Entendre, sounding somewhat flirtatiously on more than one occasion.
Final Space: Despite canon leaning to Quinn/Gary, a lot of people seem to prefer Avocato/Gary, due to the latter pair copious amount of Ho Yay and having a much more heartwarming relationship than the former.
Gravity Falls gives Dipper and Mabel, who fit pretty nicely into the Savvy Guy, Energetic Girl archetypes perfectly and are extremely close to each other. There's just one detail in that, they're brother and sister. Twins at that. No, this doesn't deter the fanbase one bit in case you were wondering, much to the creator's dismay, as he based the duo on himself and his own twin sister. The pairing even has its own Portmanteau Couple Name, Pinecest.
One of the most popular ships in the fandom, despite their age differences, is Dipper and Wendy (Wendip for short) given their incredible chemistry.
The other popular ship in the fandom happens to be Dipper/Pacifica (Dipcifica for short), which became heavily teased by the creators during the episode "Northwest Mansion Mystery" and in varioussidematerial released during and after the series.
Alternative circles of fans, like on the Archive of Our Own, have Dipper/Bill as one of the most popular couples.
Mabel/Pacifica (Mabifica) is very popular due to people liking how their personalities would work together. There's a good chunk of Ship-to-Ship Combat between it and Dipcifica fans, though a Sibling Triangle is avoided in most fanworks.
Grojband, There's a sizable fan community for Nick/Mina, who ship them because Nick is one of the nicest characters in the show and Mina is a long-suffering woobie.
That said, everyone ships Laney and Corey, with the vast majority of fan art featuring them.
Harley Quinn (2019): The producers promised that the much-anticipated pairing of Harley and Poison Ivy would ultimately happen and it did in the final episode of Season 2, but Ivy's relationship and near-marriage to the clear Romantic False Lead Kite Man got an unexpected amount of popularity among fans who found Kite Man to be a surprisingly sweet and endearing character and didn't like that the setup for Harley/Ivy involved Ivy cheating on him with Harley.
Invader Zim is a No Hugging, No Kissing show, but still has several common pairings. The most popular (but also most reviled) is the perceived Foe Yay between Zim and his rival, Dib. For a straight example, Zim and Gaz (Dib's malevolent little sister) is also extremely popular, with Dib and Tak (a one-episode wonder female Irken invader) being less popular than either of the aforementioned, but still a major presence in the fandom.
The series launched with a strong following from Korra, the main character, and Mako, as opposed to the starting couple of Mako/Asami.
Korra/Asami was a small but popular alternative to Mako/Korra and Mako/Asami during book 1. Later on in the series, a good amount of the fandom eventually gravitated towards Korrasami due to Makorra and Masami both failing and the chemistry going on between the girls. At the end, Korrasami became the Official Couple. This is actually a subversion, as by the time the ship achieved Fan-Preferred Couple status, it was the creators' preferred couple as well. This just wasn't clear at the time due to the (reasonable based on historical precedent) assumption that the writers couldn't possibly be deliberately giving the lead a same-gender romance in a children's series on Nickelodeon.
Within hours of their debut episode, Avatar Wan and Raava started getting shipped by a surprising number of fans. Helped along when one fan drew a humanized version of Raava that the newly christened ship's shippers immediately latched onto.
There are far more fanworks involving Lin and Tenzin than there are of Tenzin and his wife Pema. Tenzin is Happily Married with four kids, but a comment in an early episode caused fans to lean towards Linzin. In their youth Lin and Tenzin dated but broke up. Pema had a little to do with it, however the two were too different to work out anyway and had been growing apart even before Pema came into the picture. A large portion of Tenzin-centric works focus on his past with Lin, are outright AUs where they don't split, or have Tenzin cheat on Pema with Lin. Pema even gets hits by Die for Our Ship and is sometimes depicted as a home wrecker.
Lin and Kya have no love interests, so people tend to ship them together. Kya being confirmed to be attracted to women helped spur on the ship.
Tenzin's daughter, Jinora, is the center of two such pairings. She's usually aged-up to be closer to Opal and Korra's age (Jinorra?) and both pairings seem to be evenly split in popularity, judging from the steadily growing amount of fan art dedicated to them.
The Lion Guard fandom can't seem to make heads or tails on who to even ship Kion with. He has many times more options for significant others than any other protagonist in the whole franchise has, so nearly everyone has a different preference:
Kion and Fuli is a fairly popular ship, but it's often criticized for being an interspecies pairing. The select few who give them biological offspring typically get it worse than most.
Seeing as Jasiri has come the closest to outright with flirting with Kion so far, shipping the two was a given from the start. Though, considering she is a hyena...
Some might say shipping him with Tiifu or Zuri would be the most logical, since they're lion cubs just like he is.
Even though almost nothing is known about Rani, another lion cub character announced for season 3, she's been shipped with Kion by some already. This later gets confirmed as the Official Couple of the show, with Kion marrying Rani in the finale.
Derpy Hooves and Dr. Hooves are very popular together, to the point of the Doctor being considered the father of Derpy's fanon daughter Dinky. The episode "Slice of Life" has the Doctor has the one pony Derpy turns to and one of the few ponies that does not view her as a walking disaster (the Doctor even let's Derpy walk around his "workshop" and play around without a care) and towards the end Derpy gives the Doctor a sweet hug. Let this ship sail!
While the vast majority of the cast is shipped with everyone else, Lyra and Bon Bon tend to be paired almost exclusively which each other. Case in point, do a search for either character and you'll get almost nothing but Lyra/Bon Bon pictures, whereas if you try a similar search with any other characters you'll probably get five or six different pairings before you get past the first page. There are outliers that pair them up with other characters, of course, but the pairing is so widespread in the fandom that in most fanworks its assumed to be the case unless it's explicitly stated otherwise. When the two met up at a Ponyville market in "Putting Your Hoof Down", their saddle bags had each other's cutie mark on them And thensent over the top by their human versions' "love duet" performance in My Little Pony: Equestria Girls Rainbow Rocks. While "Slice of Life" had them constantly refer to themselves as "best friends", their constantly looking at each other with bedroom eyes and having blatantly romantic body language has many in the fandom convinced that not only has their ship sailed it is on an around-the-world journey. And in the end they became an Official Couple.
Vinyl Scratch(DJ Pon-3)×Octavia shipping is also extremely popular, with both of them being fan-favorite musicians. The episode "Slice of Life" even canonized that the two are roommates.
The introduction of the dragon princess Ember in Season 6 has seen a landslide of stories and art pairing her with Spike.
While pretty much every main character is a Launcher of a Thousand Ships and the main characters are paired in every combination, the most popular ships seem to be Dash×Pinkie, Dash×Applejack, Dash×Fluttershy, and Rarity×Applejack. These are in large part due to their chemistry and to their screentime together, especially in early episodes.
Phantom Investigators was for the most part pretty No Hugging, No Kissing among the four leads, with any romance with them only being crushes on one-shot or background characters that did not go past one episode. While the show doesn't have a large fanbase due to it's obscurity, many diehard fans of the show tend to ship Daemona and Casey. Doesn't hurt that many of their interactions could easily be read as Ship Tease, such as Daemona wrapping her arm around him at one point in "Birthday Presence" and calling him adorable at the beginning of "Were-Dog".
Ferb and Gretchen has become popular with those who have a hard time overlooking the age gap between Ferb and Vanessa (but have an easy time overlooking the fact that Ferb and Gretchen have hardly interacted at all in the show itself). Yet the very second Monty is introduced as a love interest for Vanessa, Ferbnessa becomes more popular.
There is also a sizable set of Doofenshmirtz/Linda shippers, to the point that it's a WMG that he is Phineas' father. Doesn't help that it's canon that they used to date.
Professor Utonium and Ms. Keane has a strong fan following. They were the subject of one episode late into the series, and it was thoroughly deconstructed and eventually annulled by Ms. Keane's cat, with the Professor having an aversion to cats due to one being the Big Bad of an earlier episode.
While many Randy Cunningham: 9th Grade Ninja fans ship what seems to be the intended endgame of Randy/Theresa ("Fowlham"), even more ship Randy and Howard ("Weinerham"), probably due to the show having all of the usual questionable bro closeness without so much of the "no homo" that usually comes with it.
Given that Mordecai wound up with neither of his two girlfriends, the shipping wars between the two resulted in a draw, as nobody won. Still, that hasn't stopped fans of each insisting that either Margaret or CJ should've been with him at the end. Shippers of Mordecai/CJ were especially distraught, given that Word of God claims they didn't even stay friends afterwards, despite Mordecai and Margaret continuing to be close.
Although Thomas and CJ never met, fans like pairing them together, especially from the Mordecai/Margaret fans. Some are the reasons are Thomas deserves a nice girl and it beats having the Mor/Mar fans bashing poor CJ. But since it was revealed Thomas' a Russian spy and went on the run, it's not known the current status if this ship.
Even though Rocket Power was mostly No Hugging, No Kissing, there's a large following for Twister/Reggie. It's the most commonly encountered pairing in Rocket Power fanfiction.
While the original '70s cartoon was No Hugging, No Kissing, most of the people at large assumed that Fred/Daphne were at least implied. Meanwhile remnants of Shaggy and Velma being siblings during the show's creation could have been interpreted as pairing of the two.
In the 80s the subtle hints shifted over to Shaggy/Daphne with the two even sharing a long hug in one episode. Note that several of the 1980s versions of Scooby-Doo had written Fred and Velma out of the cast, while always keeping Shaggy and (frequently) Daphne.
Since then starting with Zombie Island, Fred/Daphne started being played with more directly to a split base.
After Mystery Incorporated, many fans online began shipping Daphne and Velma, as many see Fred/Daphne as seen as overdone and boring.
Several episodes of Be Cool Scooby Doo also touch on the Shaggy/Daphne 'ship, with the more cuckoo Daphne trying to help out Shaggy with his fears or bring out the best in him and Scooby, one episode even has her pretending to be Shaggy's girlfriend for the duration of the story and seemingly enjoying it too much.
Fans of She-Ra and the Princesses of Power took no time at all to land on Adora/Catra. It's very easy to read their relationship as "girlfriends who broke up due to outside circumstances and are pretending they don't still love each other", and given the showrunners, this was most likely intended. It's seen as less a question of "were they together", and more "will they get back together", with most fans leaning towards "yes." They get together at the end of the series.
In Sidekick, Eric has a crush on Vana, but fans like him better with Mandy or Kitty instead, due to them being on the very, very short list of people who don't treat him terribly. Helped by the fact that Vana would take any opportunity to leave Eric for dead, and usually needs serious coercion to help save him.
Nedna (Ned Flanders/Edna Krabappel) is literally a fan-preferred couple: FOX held a vote to see if they should break up or become an Official Couple. Nedna won (but not before Marcia Wallace died, leaving Ned Flanders a widower once again).
Nelson/Lisa is generally considered a better future outcome than Milhouse/Lisa, by fans and voice actors alike. So much so that in The Simpsons: Tapped Out, Nelson and Lisa spend significantly more time referencing their relationship than Milhouse does expressing his crush.
Despite breaking his heart and ultimately freindzoning him in the episode I Love Lisa, there are a few fans who would still prefer Lisa date Ralph Wiggum, largely due to the synergy with level headed Simpsons women marrying dim-witted husbands. Lisa herself has imagined being married to Ralph and having several kids with him, and even remarked that Ralph being a potential U.S President wouldn't be so bad, and even liking the idea of being his first lady.
Bart/Laura Powers from the episode "New Kid On The Block" is a fan=favourite pairing due to the chemistry between the two's rebellious and fun-loving personalities, as well as Laura's promise to date Bart once he grew up a bit more.
Milhouse is often shipped with One-Shot Character Samantha Stanky from the episode "Bart's Friend Falls In Love" as a result of Milhouse's canon crush Lisa being shipped with Nelson instead and Samantha being one of the few people who's actually nice to Milhouse.
Over the seasons, Marge's relationship with Homer has gone through so many up's and down's that many fans have taken to alternate pairings instead. Marge/Maude is one of the more popular ones. The two seldom interact one-on-one and Maude was eventually Killed Off for Real, so their relationship is played as a tragic short-lived romance between two lonely housewives.
Star Wars Rebels. Kanan and Hera (Kanera) is by and far the most popular ship in the fandom. Their frequent Ship Tease moments, Team Mom and Team Dad dynamic, and the creators taking a less is more approach by focusing more on their egalitarian and supportive relationship than any romantic tropes got more or less the entire fandom shipping them long before the pairing was confirmed as romantic.
Pairing Ezra up with Princess Leia became popular because of their chemistry in the episode "A Princess on Lothal". Unlike most examples, however, this usually isn't in opposition to her canon relationship with Han but simply something that happened before they met. Most works that presume Ezra survives to meet Leia again Post-A New Hope usually have him as an Amicable Ex.
Star Wars: The Clone Wars: Ahsoka/Rex (Rexsoka) remains the most popular Ahsoka pairing, even though she has a canon love interest in Lux Bonteri. This is probably because Lux is comparatively new on the scene, and Rexsoka was already well-established in the fandom before his episode premiered in Season 3. Karen Traviss and Karen Miller's teases towards Rexsoka in the novels did not help things.
Peridot/Lapis started out as a ship passing in the night, as it was just a pairing of two unrelated but popular new characters. Then they became roommates in the third season, slowly becoming Like an Old Married Couple. On both FF.net and Archive of Our Own, their pairing has the most works dedicated to it, surpassing canon ships like Rose/Greg and Ruby/Sapphire. It is something of a controversy magnet, though.
While support for this pairing is near nonexistent everywhere else, the SU fandom on 4chan's /co/ board is very fond of Greg/Pearl, both as a present-day pairing and as an AU where he fell for her instead of Rose. For the first half of the show, this was purely a Crack Pairing thanks to Pearl absolutely loathing Greg due to having been the Romantic Runner-Up in a Love Triangle involving Steven's mother. This ship would become a little less crazy when they became friends who hang out regularly after Steven forced them to talk things out in Season 3, with the original outline for "Mr. Greg" serving as ammo for the pairing. Factory reset Pearl's devotion towards Greg in Steven Universe: The Movie also helped.
Another ship that is very popular on /co/ (and Tumblr) is Steven/Spinel, which came to vastly outshine the popularity of the canon Steven/Connie ship, with many thinking there could be a lot of bonding due to their complex histories with Pink Diamond. Plus, they just look cute together. As a result, Connie is very often the subject of Die for Our Ship from this group of fans.
Reef/Fin from Stōked is easily more popular than any other pairing on the show, even though Reef/Lo is the Official Couple as of season two.
Super Robot Monkey Team Hyperforce Go! has a weird case of this. Hints dropped in the series originally seemed to show Otto/Nova as canon, but it seemed like almost everybody in the fandom shipped Sprx/Nova. Then hints of that started to show and eventually it became the canon. A comment from one of the voice actors mixed with that the creator does pay attention to the fandom seems to hint that the coupling was changed because of this, making the FPC the Official Couple.
Since the beginning, many fans have embraced the idea of Warden/Mistress (Misden or Wardess) getting together, most of the time being aware that they are foes. As of Season 3, this does not appear possible.
Alice/Mistress shippers, even though the relationship would in likelihood be as one-sided as Warden's affections for Alice (as Alice seemed unimpressed at Mistress' change and remarked on forgetting how "needy" women can be).
Sym-Bionic Titan: The pairing of Ilana and Lance (dubbed Ilanca by the shippers) has been favored since the very first episode, despite how in the show they're posing as siblings and have other potential love interests, and the show's creator Genndy Tartakovsky, has stated in interviews that he wants their relationship to be a platonic one.
Teen Titans: Beast Boy/Raven. The creators and writers of the show repeatedly stated that the two character would never be more than Platonic Life-Partners, though such a relationship was often joked about in the tie-in comic series. The ship became increasingly popular, quickly becoming the preferred complementary ship for Starfire/Robin shippers. At the very least, a substantially large amount of people prefer it to the official canon couple of Beast Boy and Terra (the difference on FF.net is about twelvefold in the romance category). The popularity is noted in other versions of the Titans, however; the mainstream comics had them as a couple at varying points during the mid-2000s, and the animated comedy Teen Titans Go! completely embraced the pairing (while turning Robin/Starfire into a case of unrequited love), dedicating several moments and whole episodes to their relationship.
In Thunderbirds Are Go!: The most prevalent 'ship is 'Pen'N'Ink', aka the pairing of Gordon Tracy and Lady Penelope. The show has hinted at the pairing significantly over the years, with the two-parter "S.O.S" being somewhat of a pay-off. Other fans like to pair the Hood's niece, and IR member Kayo, with one of the Tracy boys, Alan in particular.
In Tiny Toon Adventures, Ensemble Dark Horse Fifi la Fume is occasionally depicted as the target of a crush by Hampton J. Pig. In the fandom, very few acknowledge this, as most prefer to portray Fifi finding love with her male feline classmate, Furrball. This stems predominantly from the fact that Fifi having a crush on Furrball is canon to one episode (although it goes nowhere, Furrball's dislike of Fifi as a Smelly Skunk has to do with her stench and he doesn't dislike her as a person), the fact that this would further Fifi's resemblance to her inspirationnote Fifi is a Gender Flipped expy of Pepé Le Pew, whose running (if somewhat reluctant) love interest is the female Penelope Cat, and the fact that Furrball is a sympathetically unlucky, unloved and abusedUnpopular Popular Character and Fifi is an Ensemble Dark Horse with a lot of love to give.
Sam and recurring villain Tim Scam also seems to be a popular ship among the fans, given that it takes up a good chunk of the Totally Spies archive on FF.net.
Transformers: Generation 1: Prowl and Jazz might well embody this. In canon, regardless of cartoon or comic, they barely interact, and the few times they do, they generally dislike each other, and yet they have hundreds of fics on FFN. There are reboots where the two are on good terms, but most of the fanfics pairing them are about the G1 characters. There doesn't seem to be any base to the pairing other than "they're both white cars from the 1984 line" and "they could have chemistry, theoretically." It gets to the point where Prowl/Jazz fans can get downright rude towards characters who do show affection toward Prowl (most famously Chromedome and the Constructicons).
By far the most popular pairing is Knock Out/Breakdown, despite Breakdown having shown interest in Airachnid.
Jack/Arcee is quite popular as well, even though Word of God denies any romantic feelings between them. But due to the Relationship Writing Fumble, it gets hinted alot that there may be some deeper feelings between them, which only gives the fans more fuel.
Given the rampant amount of Ho Yay between them on Ugly Americans, Randall/Mark is pretty popular in fan-art.
Keith and Lance in Voltron: Legendary Defender, so much so. Something like half of all Voltron fics on AO3 are these two getting together. Its only real competition is Shiro and Keith (which, though just as non-canon, also outstrips all other pairings by a pretty wide margin). They've had varying levels of Ho Yay throughout the show, but that's about it. This even earned the fandom a somewhat cold reception when Klance outtrended fellow red-and-blue gay pairing Rupphire on Tumblr, on the week that the latter pairing got married. This was emphasized in later seasons with the lion switch, where Keith becomes the leader and Lance becomes his right hand man. There is also preference from the fans due to the writers noting that they had influence from Macross, an anime with a famous Love Triangle. As of the end of the series, though, it's still non-canon.
Wander over Yonder has Wander/Lord Hater hardcore shipped, which became closely followed by Wander/Lord Dominator after the events of season two.
WordGirl: While neither couple is official, Becky/Tobey is easily more popular than Becky/Scoops.
In X-Men: Evolution, while Scott/Rogue was a favorite of many of the shows creators (and had a large fanbase to speak of), fan support for Gambit/Rogue was so popular that eventually the writers gave an entire episode devoting time to the possibility, and the last image of the series suggested they were together. Interesting fact is that the writers, in the first scene Rogue and Gambit shared, had apparently intended to insinuate a past relationship between them (or so it is claimed); fandom was strong enough that if this plan was ever in the cards, it was discarded in favour of actually developing their chemistry onscreen, even if just for one episode.