So does that mean she has a thing for Professor X?
The DC/Marvel series in the 90s gave us a short Robin/Jubilee romance which was actually quite nicely done, in a rare example of a canonical crossover ship.
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.
JLA-Avengers sees Kismet and Eternity, the avatars of the DC and Marvel Universes respectively.
Believe it or not, 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.
Oddly, Amuro (or Hiroshi) never seem to get paired up with Murrue, Tonya, or Vega. Vega's married, but the other two...
Setsuko Ohara of Super Robot Wars Z and Shinn Asuka in Z is probably the most supported pairing, if not, the prime Crossover Ship in existance, as it's one of the few that actually 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.
It's strange that Kamille is left out of any crossover shipping in Z, since he , Shinn, and Setsuko form a tighttrioafter her squad is killed by Asakim. Kamille and Shinn are best friends on Rand's route as well, so it's hard to belive the crazy fangirls haven't run away with that by now.
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.
Cassie Hack and Evil Ernie in Hack/Slash: The Final Revenge of Evil Ernie. Bomb Queen also hits on her in their crossover, but she's an Anything That Moves type.
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.
Azula left Doom, complete with a "Dear John" letter. Apparently the good Doctor has rebounded and is going out with Squirrel Girl, but rumors of Azula returning are flying around.
There is a fic pairing Ichigo Kurosaki and Asuna Kagurazaka, after they bonded over their big swords. In a bit of a subversion, both considered a romantic relationship to be too "weird" and instead opted for "friends with benefits".
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.)
And speaking of Sailor Moon, the Sailor Moon crossover category at Fanfiction.net is all aboutCrossover Ships, 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.
The 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.
The fusion of Dynasty Warriors and Samurai Warriors, aka Warriors Orochi, played this to the extreme. Now we have Cao Pi/Mitsunari, Ling Tong/Okuni, Sun Shang Xiang/Inahime, Tachibana/XingCai, and so on and so forth...
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.
All of the above are either canonical or have some... interesting Subtext.
On the other hand, an old Cartoonnetwork.com game, Cartoon Cartoons Summer Resort Part 4, has you playing matchmaker by pairing up some of the Cartoon Cartoons guys with the right girls. Said pairings as are follows: Buttercup/Dexter, Blossom/Edd, Bubbles/Courage, Deedee/Chicken, and Suzy/I.R.Baboon.
An even earlier Cartoon Network ad showed that Johnny Bravo and Velma dated, but it didn't work out. However, another ad years later showed them going to dinner, implied heavily to be romantic.
Blossom/Aku, it even has a fan-following on Deviantart.
In House of Mouse, a throwaway panel showed Jafar and Maleficent at the same table — with Mickey whispering that the two were on a date. Disney fanatics instantly took a shine to the two as a couple.
If that doesn't work out, House Of Villains and The Kingdom Keepers suggest that she and Chernabog would be great (and dark) together.
House of Mouse also gave us Hades having a bit of a crush on Maleficent. There's also potential in Black Pete, given his servant-like relationship to her in Kingdom Hearts.
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 are quite a few pictures where Rouge the Bat from Sonic series and Jewel Man from the Mega Man series are paired up probably due to their similar looks and personality traits.
Quite well, through various devices. And then there's the one Harmony/Wednesday fic, which used the common conceit that Harmony is actually Amanda from the Addams Family (both were played by Mercedes McNab).
Faith (or Buffy or Dawn) is often paired with one or more of the Winchesters. Or Alec.
The characters of Baccano seem to lend themselves curiously well to crossover shipping, particularly Luck Gandor, who to all appearances is the fandom's Launcher of a Thousand Ships and has been shipped with characters from D.Gray-Man, Gundam 00, Persona 3, and more.
Sephiroth/Kuja, however, predates Dissidia by several years.
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.
Cloud/Yuna has been popular for awhile now; a recent boom no thanks to Dead Fantasy.
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.
Zoey101, Drake & Josh, and iCarly have multiple crossover ships. Nevel/Megan is probably the most popular of these.
With the addition of Victorious, Cat/Freddie and Jade/Sam are quite popular. The idea that a Drake & Josh/iCarly crossover might happen also fuels Freddie/Megan support.
Goblin manages to hook up with Harley Quinn in I'm a Marvel, I'm a DC. It's just as messed up as it sounds and twice as funny.
And just because the creator loves doing it, he also gave us Poison Ivy and Sandman. Which makes sense if you think about it, except she'll probably cheat on him with Aquaman.
Pretty much a staple of "multifandom" Livejournal 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.
/M/ had this idea that Shinji and Noriko would make a good couple.
Artemis/Alex from the Artemis Fowl series and Alex Rider books have a surprisingly large fandom, considering they would probably hate each other.
One of the most mind-numbing, and downright offensive: Goku and famed teenage holocaust victim Anne Frank. Seriously, someone went there. Sage has the horrid details.
One of the strips implied that apparently celestial administration ships Cruella De Vil and Sauron
Thanks in no small part to a little fanfic called The Way of Things, Rose/DI Carlisle has an impressive following.
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.
Ladies and gentlemen, prepare to clean up your brain matter after Your Head Asplode from witnessing the greatest crossover pairing ever conceived: B/ASH, otherwise known as Buffy Summers/Ash Williams. BEHOLD!
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.
Bec/Amaterasu gets shipped a bit among the Homestuck fandom. Also counts as a Theme Pairing because they're both dogs/wolves with godlike powers.
This same trailer has Morrigan stabbing Deadpool in the ass with her tentacles and Chris Redfield performing a Diving Save to prevent Morrigan from falling to her death after Iron Man gets a sneak attack in on her. These are used as "evidence" for Chris/Morrigan and (humorously so) Deadpool/Morrigan.
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."
Felicia and Super Skrull appeared together on one game-affiliated t-shirt. Cue the fans on Capcom's official forums shipping them together.
And thanks to the Episode 4 trailer, Haggar/Felicia.
Felicia also has a humorous win quote against Deadpool: "No, I don't care how much catnip you have, I'm not getting into the car with you!" How you interpret this one is up to you.
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.
"Tall, blond, and handsome—you're my type of guy... But do you have to carry that hammer everywhere?"
In his quote at the win screen, Viewtiful Joe finds She-Hulk to be attractive. The same could be same for Spencer, who goes on a sort-of-but-not-quite-date with her in his ending.
she has some Les Yay-ish intros with X-23, Tron, and Phoenix, as well as some ambiguous quotes towards Magneto
is up to six 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.
Keep in mind that 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.
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
There was once a movement on LiveJournal to pair Captain JackHarkness with every single fictional character ever. Unsurprisingly, it didn't complete its task, and nowadays seems to have lost steam altogether.
This fan fic has Vitani/Alex, when Vitani gets captured and sent to the Central Park Zoo. (It makes a lot more sense then most of the stuff on this page.)
Kirby and Sylar had a rather squicky relationship that ultimantly resulted in both of them becoming less evil that was until Kirby was killed leading Sylar into a Roaring Rampage of Revenge.
Jenny Sparks had a one night stand with Intergra at some point previous to the start of the game.
C.C. was Spider Jerusalam's first wife they got divorced for unknown reasons that involve Spider cheating on her, Spider refusing to accept Geass and Spider always wanting caribou eyes on pizza.
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?
Ika Musume and Neko Musume. Why? That's simple: Cats LOVES fish and Ika Musume is a squid.
Another weird crossover pairing is Airi with Ike. The reason? Maybe because both characters belongs to series with a fantasy setting.
in this Spider-Man/Danny Phantom crossover [12] 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.
Soujiro Seta x Beyond Birthday is a wonderful example for a very self-destructive and dark Crossover Ship [13]. Still most videos of the creator make it seem differently... and very pink [14][15]
Want a Manipulative Bastard pair? Look no further than Lelouch Lamperouge/Alex Russo. Since they both have powers (Lelouch has Geass, Alex has Magic), and love to manipulate anyone, they'll manipulate just about everything to oblivion.
Alexander Anderson/Ciel. Bayonet/sword throwing members of a secret Catholic organization dedicated to eradicating Vampires? Sign me up. Comes with awesome fanart◊.
Ichigo Kurosaki/Gintoki Sakata has some merit, considering even their seiyuu ship-teased and co-hosted during a radio special.
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.