The DC/Marvel series in the 90s gave us a short Robin (Batman)/Jubilee (X-Men) romance which was quite nicely done, in a rare example of a canonical crossover ship. note Made Hilarious in Hindsight due to the fact that the two were combined in the Amalgam Universe to become Sparrow.
One of the one-issue "giant crossovers" from the 1980s teased the readers with hints of Beast Boy (then "Changeling")/Kitty Pride. Another played with the concept, possibly to parody it, by having Spider-Man ask Wonder Woman if she thought it was too early in their relationship to consider marriage (they had met, and briefly fought, only a few minutes earlier).
A Wolverine/Witchblade crossover licensed by Marvel and Top Cow started with Logan and Sarah Pezzini getting married! Obviously it didn't last.
The SyFy channel has embraced this trope, pairing up Claudia and Fargo in their Warehouse13 / EUReKA crossover episodes. At first, it just seems like a mutual crush that won't go anywhere, but then, Claudia's boyfriend breaks up with her. Then, Claudia comes to Eureka. As they search for what's causing that week's problems, there is some flirting, and after being saved from a minefield, we get a full-blown makeout.
Setsuko Ohara of Super Robot Wars Z and Shinn Asuka of Mobile Suit Gundam SEED Destiny in Z is probably the most supported pairing, if not, the prime Crossover Ship in existence, as it's one of the few that makes a lot of sense considering their close relationship in-game. Because of the presence of Setsuko in the game and how Gundam SEED Destiny's events are rolled out in her route, Shinn's glaring flaws from the original story are actually fixed, or at least mellow them down. It helps that Setsuko can relate with Shinn on an emotional level. Arguably, this fanon pairing has become the best example of this trope. It helps that they actually do become very close in the game.
In a weirder example, in the OG series, the Wildfalken & Wildwurger mechs were created by mating weapons and armor derived from the Pact series' Alteisen & Weissritter to Alpha series Huckebein frames.
In a spin-off series in the Eighties and Nineties, it was impled that Nancy Drew and Frank Hardy had a crush on each other (Poor Ned and Callie). Similarly, there was a much more faint flirtation between Bess Marvin and Joe Hardy.
Especially pairing Usagi with some other guy besides Mamoru. There are even two dedicated categories for Gundam Wing and Dragon Ball Z crossovers, mostly because the shows all aired on the Toonami block around the same time.
Usagi tends to get paired up with a lot of characters from other series, as this YouTube video proves.
Sailor Moon girls have an annoyingly frequent habit of getting paired with the Saint Seiya boys. There are reasons, of course-they're roughly equal in number, and there are so few females in SaintSeiya that if you wanted a het ship you'd probably have to use a crossover. Also, if you try you can get characters with matching hair colours to pair up together...
There are a surprising number of Sailor Moon/X-Men crossovers that run the gamut of serious to silly but one of the most consistent aspects is the shipping Sailor Mercury/Nightcrawler.
There is plenty of people who ship Jack Skellington from The Nightmare Before Christmas with Emily, the Corpse Bride from the title. For people who like their fan fic slashed, there is Jack Skellington/Victor Van Dort, Emily's very much alive "husband" for a time. Corpse Bride Emily gets paired with Sally, a cute rag doll created by a Mad Scientist.
There's rather disturbing pairing: Jack Skellington of The Nightmare before Christmas and Coraline of Coraline. That's right, an eleven-year-old girl with a fully adult skeleton.
It's only a little exaggeration to say that characters from Harry Potter get shipped with every other available fandom out there. Especially Harry Potter gets paired with female characters, but there is also lots of Slash.
There's an awful lot of Harry/Buffy fiction out there.
It's definitely a thing in Jane Austen's fandom to Pair the Spares, and very often cross-novels. It helps that the world of Jane Austen's books is always very similar — pastoral and almost-idyllic version of Regency England. It's not uncommon for characters like good-natured but stupid and extremely wealthy Mr Rushworth of Mansfield Park, divorced from his cheating wife, to be paired with Miss Bingley from Pride and Prejudice who was always after money, or some ship him with Mary Bennet, who, as some fans believe, deserves more attention and a wealthy husband.
There is one extremely weird example of, of all things, River Tam being shipped with Heat. It stemmed from the two encountering one another during a multi-author Mega Crossover, with Heat equating River with Sera. She latched on to him because he was protective of her, he latched onto her because she reminded him of Sera. Things got even weirder from there, with Heat doing his cannibalism thing and River being not-at-all freaked out about it. The thing had a rather powerful and sad Did Not Get the GirlDowner Ending, as there wasn't any sex, just very rough kissing (with biting and some bloodplay involved) and a whole lot of insanity, and the two had to split apart at the end of it because Heat refused to take River back to a world as screwed up as his and had no place in hers. It was really well-done, especially on the part of the author writing Heat's part of the story.
There are a few Buffy/Firefly crossover fics that ship Spike with River Tam. This works remarkably well as crossovers go. Spike, who spent over a hundred years with Drusilla and was then haunted by the First Evil, has significant experience with people who "see things" and is in a better position to relate to River than anybody in Firefly canon. Spike's immortality makes it easy to rationalize his presence in the Firefly universe: he just lives long enough to leave Earth-That-Was with the rest of humanity. Then there's the fact that having been born in Earth-That-Was makes him an (un)living memory of a time that is seen as legendary by the inhabitants of the 'Verse.
There's a growing number of River Tam (Firefly) and Riddick fics.
Thanks in no small part to a little fanfic called The Way of Things, Rose (Doctor Who)/ DI Carlisle (Blackpool) has an impressive following.
There was once a movement on LiveJournal to pair Captain Jack Harkness of Torchwood and Doctor Who with every single fictional character ever. Unsurprisingly, it didn't complete its task, and later it lost steam altogether.
Buffy the Vampire Slayer has sometimes been shipped with Dean Winchester, or sometimes with Sam. So has Faith, for that matter, though both Slayers more likely end up with the older brother. In a case of Pair the Spares, if Buffy is with Dean then Dawn will likely be shipped with Sam. The pairing is strengthened by the idea that the two universe actually mess together rather well, with the metaphysic differences not too hard to Handwave due to having a number of common elements.
Dean (Supernatural) gets around. The most popular het ships are Dean and Chloe from Smallville and Dean/Hermione (Harry Potter).
It can be quite safely stated that there is an entire sub-category of Smallville fanfiction devoted to the idea of Chloe moving to Gotham City (often after the author has Chloe realize that Clark/Jimmy/whoever "isn't good enough for her") and then meeting and falling in love with Batman. Usually, Chloe ends up either becoming Mission Control at the Batcave or she undergoes Xenafication and becomes Batgirl or Batwoman (or occassionally Catwoman) and ends up fighting crime alongside Bruce on the Gotham City rooftops. Either way, she can usually work the Batcomputer better than Bruce can, proves to be his match in fighting skills, and if Bruce is still "in denial" about his feelings for her, Alfred will usually advise him to "open his eyes and see what's right in front of him."
Chloe (Smallville) is a Launcher of a Thousand Ships (possibly due to the huge amount of fanfic writers who seem to very strongly relate to her personality), and another hugely popular Smallville crossover ship is to pair up Chloe with either Dean or Sam from Supernatural (or, y'know, both). The Chloe/Dean ship seems to be more popular than Chloe/Sam for whatever reason.
Martin Crieff (Cabin Pressure) / Molly Hooper (Sherlock) has a modest following. Cabin Pressure and Sherlock are Friendly Fandoms that are easily crossed over. Depending on the execution, it can be a combination of Theme Pairing and Throw the Dog a Bone, as both Martin and Molly are rather unfortunate in many aspects of their lives and overdue for something nice to happen to them. (There's also the fact that Molly pines after Sherlock, who's played by Benedict Cumberbatch, the same guy who played Martin Crieff.) There also seems to be a small but steadily increasing number of fans of Martin and one episode character Henry Knight.
This fic crosses over Stargate SG-1 and Torchwood. Pairings include Jack Harkness/Daniel, Jack O'Neill/Ianto, Owen/Anise/Freya, and Gwen/MALP. Bonus points for the title being abbreviated to CR:ACK.
Tumblr once exploded with Norman/Dipper fanart (Norman of Para Norman) and Dipper of Gravity Falls) fanart tagged under Parapines. This mostly seems to stem from their supernatural connections and general adorableness. So far, the art remains rather tame and limited to G-rated interactions like kissing. Examples: .
Lisa Simpson from The Simpsons is the Launcher of a Thousand Ships in some crossover fics. She's been paired up with, to name a few, Dalek Sec, Starscream, Waspinator, Jack Harkness and Randall Boggs of all characters, although, with the exception of Captain Jack, those were all subtext.
Saber and Kohaku.No, really. They're adorable, actually. Kohaku loves to cook, Saber loves to eat; and they both understand wanting to live their lives over.
Azula / Wall-E. Because there is no better way to help cure Azula of her Villainous Breakdown. (This is a friendship pairing, not a romantic one, mostly because if EVE found out, Azula would not survive the night.)
Wilbur / Violet has gained a small, yet growing following. Figment Jedi believes he might have been the first to think of it, in response to seeing Wilbur encountering a Violet look-alike in a storyboard featured in the Art of Meet the Robinsons book.
Cloud / Terra has a following as well, as do Firion/Terra and Firion/Cloud. Why these three? Besides Cloud's interactions with both of them, Dissidia heavily implies that Firion and Terra remind Cloud of Zack and Aerith, and their personalities are reminiscent of them as well. It didn't take long for shippers to go from there. It helps Terra has no canon love interest.
The prequel, Duodecim, gives us Firion/Lightning due to their mutual bonding over flowers. Comes complete with Ship Tease, as Cecil (the only canonically married member of Team Cosmos) plays the role of Firion's wingman and takes his embarassment over wanting to talk to Lightning as romantic interest.
A staple of "multifandom" Journal Roleplay games. Since these games dump characters together into one common setting, they can become Serious Business (particularly since LJRP itself is serious business), although they're often suggested for simple crack as well.
Pairing Noctis of Final Fantasy Versus XIII and Lightning of Final Fantasy XIII (which, despite names, are set it totally different universes) is surprisingly popular, and has been even before the release of either game, if FF.net is any indicator.
Correction: JediAnnSolo has repeatedly stated that Sandy/Shadow is not Agency canon. However, this hasn't stopped her from admitting that they make a good couple or stopped her and her fans from pairing the two up.
Morrigan seems to be switch-hitting between Tony and Chris in the openings. In the Episode 2 trailer, after Iron Man saves Viewtiful Joe but fails to do the same for Amaterasu, Morrigan saves Ammy and then blows a kiss to Iron Man. In the Episode 4 trailer, the last shot is a still showing all of heroes and villains duking it out... except for Morrigan, who is seen lovingly wrapping her arms around a flustered Chris, perhaps as a way ofsaying thanks for saving her in Episode 1.
There's also been a boom in Dante/Morrigan (which had been around at least a few years prior to MvC3); it's probably Dante's most popular ship next to/alongside Dante/Bayonetta.
In a Mythology Gag to Dante's meeting with Nevan (yet another Horny Devil) in Devil May Cry 3, the two are seen flirting if they're on point against one another. Dante's also says, "Mmm, baby. I love it when a girl gets violent!" at his win screen should he defeat Morrigan last in battle.
In C. Viper's reveal trailer, Iron Man is hitting on C. Viper in the pre-match intro, causing some to ship them as well. Iron Man and Morrigan seem to launch ships left and right.
Well, actually, Iron Man hits on every female in this game not named Amaterasu. This includes Tron Bonne and X-23, who are respectively 14 and 16, as well as Hsien-Ko, who is (technicallyspeaking) dead. Fans jokingly suggest that the only reason he doesn't go after Ammy is because he doesn't know that Ammy is a she. Should he win against any of them, he muses, "Told you... a nice candlelight dinner would've been better." Should he win against Morrigan, his quote at the win screen reads as such:
"I think we can sort out our differences over dinner. I'll have the best chefs flown in."
This one technically isn't a crossover ship as the two exist in the same continuity. Though it is pure crack, as aside from the age difference (she's 16, Hulk's pushing 40), the one time these two have met involved Hulk beating the hell out of her friends and throwing her through a building.
And another one for Morrigan. She apparently has a fancy for Wolverine (her quote at the win screen reads, "You have a beastly charm I just find so, so intriguing"). She also cameos in his ending as an exotic dancer trying to seduce him. Wolverine relents to her whimsy... but not before he finishes his drink.
Crossover Shipping in this seriesactually happened beforeMvC3. As early as Marvel vs. Capcom 1 did Gambit's ending have him flirting with none other than Morrigan (her total number of ships, excluding a few dubious examples in 3note she has some Les Yay-ish intros with X-23, Tron, and Phoenix, as well as some ambiguous quotes towards Magneto, is up to eight right now, if you lost count). Before anything can get off of the ground, Rogue swoops in to carry Gambit away, much to Morrigan's displeasure.
Shuma-Gorath displays a creepy fondness for Hsien-Ko, going as far as to propose to make her his bride. Also, Morrigan herself shows an interest in Shuma's tentacles.
In Ultimate, Morrigan blatantly hits onPhoenix Wright. Blatantly. And then there's Rocket Raccoon having the hots for Ammy... 95% of the examples above come from the game itself. This isn't even getting into Fan Art. Marvel vs. Capcom 3: If it breathes, this game will ship it.
Tails/Klonoa seems to be a relatively popular one amongst the Furry Fandom, perhaps inspired by a certain doujinshi featuring the two... ehm, hanging out after work. That the two already looked similar doesn't hurt, either.
Damon Salvatore/Blair Waldorf shouldn't work, but the reasonably large number of Youtube videos beg to differ
Katara / Sasuke: It's like Zutara with fifty percent less plausibility~!
Sometimes you go for obvious subjects, but sometimes some authors want to make up perverted situations that normally don't exist. How about a hentai fanfic featuring Cecilia and Noblesse Oblige or Harken Browning making Cecilia wear Kaguya's stripperific outfit just to bang her in it?
in this Spider-Man/Danny Phantom crossover  the author pairs Valerie Grey and Johnny Storm. kinda squick-ish because Valerie's in high school and Johnny is supposed to be Peter's age (if not a year older) which leaves quite a large age gap.
Bayonetta x Dante. The rivals are not left out either: Jeanne x Vergil.
Bayonetta is also frequently paired up with Kratos as well. And as for a friendly but not romantic pairing, Bayonetta x Juliet Starling.
Anders / Kain has been sighted (the fic in question had them meeting in the Fade somehow). Maybe it makes some kind of cracky sense given their common status as party members straddling the hero/villain line, but that's about it.