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.
Reef/Fin from Stoked is easily more popular than any other pairing on the show, even though Reef/Lo is the Official Couple as of season two.
Despite both Ben and Gwen receiving love interests in Ben 10: Alien Force (potential or otherwise), support for Cousinshipping has not waned in the slightest. Why should it? Gwen herself says Julie should find Ben attractive because he's "funny, sensitive, and well-mannered... unlike some people I know." Not to mention Julie being widely seen as a Satellite Love Interest; Gwen at least was fortunate enough to get officially paired with an actual character.
Well, according to FF.net, four of five most favourited romance stories are Ben/Kevin (Ho Yay and Foe Yay). Then again, you can guess what kind of fan these bunch of writers writers are.
Not to mention Craig and Tweek; they are the second most popular pairing (after Stan and Kyle) which is especially surprising considering that they only openly interacted in in one episodenote Where they were manipulated into beating the crap out of each other. Tweek was shown in a nonspeaking cameo as a member of Craig's gang in a later episode, but most use the fight as the primary basis.
For some bizarre reason Jane also gets paired up with Mr. D of all people fairly often. Apparently many fans took a small scene in Just Add Water where he hesitates while coming up with a reason to give away his poker chips to her to stave off a relapse of his gambling addiction not as him struggling to find something nice to say about an ignorant stoner chick who always sleeps through his class but as him thinking "Oh shit, how can I tell her I think she's hot and still keep my job?" Amusingly enough, it may be worth noting that many of the shows fans are actually teachers and thus their interpretations of the Lawndale High faculty's characters are not without merit. Chances are they speak from experience...
Meanwhile, fics taking place before Daria moved to Maryland often pair her with Earl, a gun-toting JD based on her strangely breezy attempt to exchange banter with him in the middle of a gunfight in the episode Incognito.
There are also those fans who think Goliath should hook back up with his Psycho Ex-Girlfriend Demona, despite the fact that she's tried to kill him several times for not agreeing with her. Apparently that's Goliath's fault.
Beast Boy/Raven shippers in Teen Titans. The creators of the show repeatedly stated that Beast Boy/Raven would never happen, yet it was an increasingly popular and a preferred complementary ship for Starfire/Robin shippers. At the very least a substantially large amount of people preferred it to the official canon couple of Beast Boy and Terra (the difference on FF.net is about twelvefold in the romance category).
The ironic thing is, the creators didn't want Cyborg and Bumblebee to seem like a case of Pair the Spares, so they made the two characters initially really dislike each other to go against this, but the Belligerent Sexual Tension that resulted is one of the reasons the pairing is so popular.
Cyborg is also often paired with Jinx (in fact, OT3 of them doesn't seem that uncommon). The pairing search actually shows that to be more popular than Cy/Bee (despite Jinx being paired with Kid Flash inside the show - it should be noted that Cy/Jinx is far from catching up with KF/Jinx), but it's difficult to judge since Cyborg is usually in a secondary pairing.
It should be noted that Kid Flash and Jinx didn't become a pairing until midway through the final season, so it would make sense why there would be so many Cyborg/Jinx fics beforehand (as their potentiality as a couple was touched on in Season 3).
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 on-and-off canon girlfriend Dana Tan, as she's the least developed character of the three. As a matter of fact, in the Season One DVD Behind the Scenes featurette, it is discovered that Alan Burnett actually 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."
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. The couple gets tons of fanart and fanfiction, some of which can be, erhem, erotica.
The Simpsons has fans that are not as shipping-oriented as some other shows, but there are several of these. For example, Lisa/Nelson is vastly preferred to the edging-towards canon Lisa/Milhouse, presumably due to Milhouse being an annoying Stalker with a Crush.
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.
Ironically, though Sprx/Nova is still the main fandom ship, there are now more Otto/Nova shippers around filling the FPC bill.
This pairing was actually 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.
The Powerpuff/Rowdyruff shipping was lampshaded in season six's "City Of Clipsville," which was intended as a Take That to the shippers. It was actually embraced by the shippers.
Chip/Gadget in Chip 'n Dale Rescue Rangers, to the point where Portmanteau Couple Names aren't necessary anymore because the only terms needed are "pro" (for being in favor of Chip/Gadget) and "anti" (for explicitly opposing this ship, regardless of alternatives). Well, okay, and Dale/Foxglove.
Despite Word of God stating that Jessie from Jonny Quest: The Real Adventures was not created as a love interest for any of the characters, an overwhelming majority of the fandom ships her with Jonny. There's also a smaller group that ships her with Hadji. This is probably due to massive amounts of Ship Tease for both ships.
That's the second season. According to the Word of God from the first season, Jonny and Jessie were to be romantically linked just around the corner. It's in the first season writers bible and on the DVD extra, oddly enough.
It goes a bit beyond Ship Tease when you have the characters kiss while possessed by a pair of ghosts, then keep kissing for ten seconds after the ghosts leave. Of course, Jonny and Jessie proceed to pretend they didn't realize they'd regained control of their bodies until Hadji pointed it out.
On Tiny Toon Adventures, Fifi la Fume's occasional official love interest is Hamton J. Pig, mostly because of Pair the Spares. However, a quick search on Deviant ART reveals that a sizable portion of the fandom prefers to ship Fifi with either of her one-time romantic chase victims, Calamity Coyote or Furrball Cat, the latter likely due to her predecessor Pepe le Pew being officially paired with Penelope Pussycat.
There are no pairings in The Zeta Project, but fandom loves Zeta and Ro together as a pairing. It's actually a challenge to find fanfics that aren't Zeta/Ro.
Number 1 (Nigel)/Number 5 (Abby) from Codename: Kids Next Door are a significantly more popular ship than the canonic Number 2 (Hoagie)/Number 5 and seems to be on the same level of popularity as the canon Wally/Kuki.
Before the increasing Ship Tease in later seasons solidified Wally/Kuki as an Official Couple, they were this in the first season as well, with only one Day in the Limelight episode with each other that could remotely be considered shippy. This episode, "Operation OFFICE," is widely hailed by their shippers as the episode that got them interested in the ship in the first place.
Numbah 1/Numbah 362 (Rachel McKenzie) is another popular pairing. Many assumed this 'ship would sail after Nigel and Lizzie's break-up in the final season, but Nigel's promotion to the Galactic Kids Next Door sunk it instead, still, that hasn't stopped many fanfic authors sending Rachel off into the stars in pursuit of 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.
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.
Although the show often dabbles in Ho Yay and Ship Tease, The Penguins of Madagascar doesn't really have any canon pairings that last. However, Skipper/Marlene is by far the most common pairing among fans, which time and again proves unsinkable. The two episodes (three if you count "Otter Gone Wild") where one of the pair gets a trial run with another romantic interest act, if anything, as fuel for the fire for Skilene shippers. Not that there's very much canon at all to support it.
Sym-Bionic Titan: The pairing of Ilana and Lance (dubbed Ilanca by the shippers) has been favored since the very first episode, despite the fact that in the show they're posing as siblings and have other potential love interests. Not to mention that the show's creator Genndy Tartakovsky, has stated in interviews that he wants their relationship to be a platonic one.
Star Wars: The Clone Wars: Ahsoka/Rex (or Rexsoka, if you wish) remains the most popular Ahsoka pairing, even though she has a canon love interest in the form of 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.
Ahsoka is also shipped with Anakin, and even Senator Chu-Chi.
While the vast majority of the cast is shipped with pretty much everyone else, Lyra and Bon Bon tend to be paired almost exclusively which each other. Case in point, do a search for "Lyra, shipping" on Derpibooru, 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.
Vinyl Scratch(DJ-Pon3)/Octavia shipping is also extremely popular, with both of them being fan favorite musicians.
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.
By far the most popular pairing on Transformers Prime (if one is a yaoi fan, anyway) is Knock Out/Breakdown, despite Breakdown having shown interest in Airachnid.
Pretty much any yaoi pairing that isn't Chromedome/Rewind or Mirage/Megatron is doomed to this for now, since the franchise in general is still primarily for young boys. Of course, G1Prowl and Jazz might well embody this. In canon, they barely interacted and when they do, they (usually) hate each other. Last count on FFN for Jazz/Prowl fics? 411.
As of the season 4 premiere 'Hot To The Touch', it looks like Finn/Princess Bubblegum of Adventure Time seems set on becoming this, considering that Finn now has shifted from his Precocious Crush on PB to a Star-Crossed Lovers scenario with Flame Princess. One could also make a case for Finn/Marceline, considering that a number of fans still support it even when Marceline herself harpooned the possibility way back in Season 2. Les Yay wise it's Bubblegum/Marceline, helped by their buckets of Ship Tease in 'What Was Missing' followed by more in 'Sky Witch'.
Meanwhile, Fionna in the Rule 63 episode has a crush on Prince Gumball, but most fans like to ship her with Marshall Lee, especially after 'Bad Little Boy', or even Gumball with Marshall Lee due to the Les Yay their counterparts have.
El Tigre has El Tigre and Black Cuervo. It was so popular 'Tigre + Cuervo Forever', a catch phrase for the ET/BC 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.
In Sidekick Eric has a crush on Vana, but fans like him better with Mandy or Kitty instead.
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.
Yet the very second Monty is introduced as a love interest for Vanessa, Ferbnessa becomes more popular.
Scooby-Doo fans have "Fraphne" (Fred and Daphne, based on their Mystery Incoporated relationship) and/or "Shaphne" (Shaggy and Daphne, from their 13 Ghosts days).
Actually, Fraphne is earlier than the Mystery Incorporated show. Think about the 2002 and 2004 live-action movies.
Also, in the Scooby Doo section on Fanfiction Dot Net, most of the romance fics contain Fraphne and/or "Shelma" (Shaggy and Velma). Shaphne is the third most popular Het pairing and "Frelma" (Fred and Velma) is fourth.
Happy Tree Friends has Flippy and Flaky as a favorite pairing. This is despite all the times Fliqpy has killed Flaky, and Flaky even stabbed Flippy once. Hell, people aren't even certain what gender Flaky is, but it looks like ever since "Without A Hitch" the writers have given in to fanon.
Since the beginning of Superjail!, many fans have embraced the idea of Warden/Mistress (Misden or Wardess) getting together, most of the time being aware that they are foes. Many fanfics have depicted them falling in love slowly and realizing that they were meant to be. Unfortunately, as of Season 3, this does not appear possible.
Although the same season 3 premiere also created a faction of 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).
Despite their rather limited interaction, Dipper and Candy from have quite a bit of fanart.
Although the show is told from Dipper's perspective which wants you to root for Dipper/Wendy, most fans go for Robbie/Wendy. This pairing was canon for a bit of the series, but as of episode 17 it is unclear whether the two will get back together.
In 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. There's also a surprising number of fanart for them.
That said pretty much everyone ships Laney and Corey, pretty much the vast majority of fan art features these two.
The Hefty/Smurfette fan shipping in The Smurfs even went so far as to have an episode "Hefty's Wheelsmurfer" be named "Fortachon y Pitufina" in the Spanish dub, despite the episode having nothing to do with Hefty and Smurfette in any fashion of a relationship together.
So far there is no Love Interest for anyone in Wander Over Yonder, but Wander/Lord Hater is already being hardcore shipped. Wander/Sylvia is gaining popularity, too.