In The Seventies and The Eighties, X-Men's Mystique and her "friend" Destiny fell into this trope - with comics now subject to fewer restrictions, however, current references to Destiny (still posthumous after twenty years!) make no attempt to hide that she and Mystique were lovers. Late in Chris Claremont's first run on the series, he has the Shadow King refer to Destiny as Mystique's "leman," an archaic term for lover, paramour, or spouse. (Thank you, gayleague.org )
It was actually Claremont's plan at one point to reveal that Mystique was not Nightcrawler's mother, but his father, having impregnated Destiny while in the form of a man. The editors nixed this idea. But considering the enraged reaction of the fans to the revelation of Kurt's real father, it has been suggested that it be retconned to the truth.
In various incarnations of the X-Men, there is definite... chemistry between Professor X and Magneto, even to the point of them cracking open a bottle of red wine and discussing philosophy on their(!) balcony in Excalibur, series 2 issue 2. Charles has agreed to help Erik rebuild Genosha, so the two find it beneficial to SHARE A HOUSE! We get many scenes of domestic bliss with the two, such as Erik cooking breakfast for both of them.
In fact, in the final episode of the X-Men animated series, Jean asks "Did you love Charles Xavier?"; Erik's response is to be outraged that she could doubt it.
In the Ultimate universe, Professor Xavier says outright that he left his wife and family to be with Erik. Plus, caption box dialogue saying they were closer than brothers because of their uber-powers.
Their flashback with kid-Jean in the third movie is pretty close to a couple considering adopting a child. Sir Ian McKellen and James McAvoy both ship it. The latter referred to First Class as a love story and...well, just check out that quote at the top.
And the part in First Class where Erik is practically cuddling him. Okay, it loses something because Charles has just gotten the injury that will put him in a wheelchair forever, and it was Erik's (accidental) fault, but it still has the highest "are you sure he's not the love interest?" quotient in the movieverse.
Though the druggie psycho Magneto of the "Planet X" arc was retconned into being an impostor in an Author's Saving Throw, he was intended to be the real Magneto when it was written... so you gotta wonder why Mags, while in full-on baby-eating mode, saw fit to not kill Xavier, but instead... keep him unconscious and naked in a tank of something-or-other. (It's totally transparent, too. Magneto has an unobstructed view of Charles' ass.) He planned to release him once all humans are wiped out, and was looking forward to Charles someday looking over the new world and agreeing with him. At his most whacked-out, Mags still wanted to live happily ever after with Charles. Post-retcon, we can say the impostor got at least one thing right.
There's a 2012 story in Uncanny X-Men featuring the last two members of a species called the Apex. One of them is a benevolent yet often condescending scientist. The other is an arrogant, vengeful man grieving for his people. They've been torn apart by the latter's madness and their differing ideas about how to care for the legacy of their species. They are also in love. Sound like anyone we know?
Of course, they've also been shown to have female love interests in the comics, cartoons and cinema (Xavier with Lilandra and Moira MacTaggert, Magneto with his first wife and later Rogue of all X-Women) so perhaps Ambiguously Bisexual is a better fit.
The Claremont-written novelization of the third X-Men movie had Iceman giving Angel his codename because of his unnatural beauty, which he goes on about in narration for some time. Of course, canonically, Angel isjust that angelic-looking (even if not every comic artist manages to pull it off.)
Dani does have the superpower of mentally bonding with animals and Rahne is a werewolf. Still...
This is pretty clear: Dani: '-you're not alone. Moira loves you, and I-' Rahne: 'I know. But that doesn't make me ache any the less.'
Whenever I read New Mutants issues by Claremont, I have the feeling that Illyana crushes on Kitty, and Warlock on Cypher. The latter also works on the last New Mutants series.
Although Warlock belongs to an asexually reproducing race and thus is a "he" only by default.
Don't forget Kitty and Rachel. In Claremont's later run on Uncanny, when Rachel discovers that Colossus is back with Kitty, she storms out of their (Kitty and Rachel's) shared room and acts all mopey and depressed.
And let's not forget the overly friendly way she hugs Kitty in the X-Women one-shot. Guess who wrote said one-shot.
Warlock's love for Cypher played a part in the sad story of Earth-8545, where Warlock fused with Doug Ramsey in a last-ditch attempt to cure him of the Legacy Virus - and instead ended up turning almost every human and mutant on the planet into cyber-zombies.
Wolverine/Gambit and Wolverine/Cyclops is lampshaded by Emma Frost, who in one issue comments on how Wolverine and Cyclops have a "Rad Bromance."
While it could be interpreted as the actions of two men who have known each other since they were teenagers, Angel does seem pretty fond of randomly picking Cyclops up and flying off with him, and Cyclops seems more prone to affectionate physical contact with Warren, and to smiling. Also behold Old Married Couple Angel and Cyclops: ◊
Speaking of Claremont and Les Yay, let's not forget Spider-Woman (Jessica Drew) and Lindsey McCabe.
Or Jessica Drew and Carol Danvers. Or Kitty and her many predatory older women. Or... you know, let's just not forget Claremont and leave it at that.
Or Jessica Drew and Sybil Dvorak, or Jessica Drew and Nekra Sinclair...
And, more recently, the Psylocke miniseries starts with Dazzler riding around on the back of Betsy's motorcycle. Later, when he's trying to persuade Betsy to kill him, Matsu'o threatens:
"I won't stop. Your brother. Warren Worthington. Alison Blaire... anyone and everyone you care about will die."
Just to be clear, that's her twin brother (with whom she is naturally extremely close), the man with whom she was canonically in love for years (and who a large section of the fandom thought she was going to marry), and... the lady she's just started hanging around with, for the first time since they were both written by Chris Claremont.
When Rob Liefield and Fabian Nicieza wrote X-Force in the 90s, it was a catalog of testosterone, with Shatterstar, the Mojoverse warrior who was interested only in fighting. When Nicieza took over after Liefeld left, Shatterstar began figuring outt human emotions and struck up a friendship with fellow teammate Rictor. Jeph Loeb took that one step further, giving Shatterstar a very obvious crush on Rictor and developing a subtext between the two men that eventually became difficult to ignore and a LGBT Fanbase ensued (detailed extensively here). Years later, Peter David writing X-Factor reunited the pair and had them become a canon couple, to the disapproval of Liefield who said that his vision of Shatterstar was as a 'gladiator' and 'Spartan', apparently precluding him from homosexuality.
I guess Liefeld knows about as much about the Spartans as he does human anatomy.
In a 2005 story (Rogue vol. 3 #7-12) Tony Bedard established that back in the really old days (the flashback part of the story is set before Sunfire's first appearance, X-Men #64 (1970)) a 17-year-old Rogue was really close friends with a memory-stealing female mutant called Blindspot who also happens to be immune to her absorption power. To this day Blindspot loves to cuddle up with one of Rogue's old costumes, and at the end of the story Rogue gives her the one she then was wearing in return for having her memories restored.
The recent X-Women one shot by Claremont was written just so he could make it clear that Emma Frost, Rogue, Psylocke, Kitty Pryde and Rachel Summers are all lesbian/bisexual. The whole comic from start to finish is panel after panel of poses, lines of dialogue, scenes, and character moments that make it clear ALL these characters fancy the pants of each other and are shagging like bunnies when the "Camera" is off them.
The Colleen Coover back-up strips from X-Men: First Class were noted for some subtle Les Yay between Jean Grey and Wanda Maximoff. The fact that Coover herself is an out bisexual and was best known for girl-girl erotic comics previously didn't hurt.
In The Nineties, the X-Men were a metaphor for being gay. There was even a mutant AIDS.
Maybe even now. Matt Fraction made them live near San Francisco...
The X-Men made San Francisco a temporary base in the early days when they couldn't go back to Xavier's mansion for a while. And this back in the 80s.
In the recent X-23 comics, fandom went crazy over this little scene between Jubilee,who happens to be a vampire (better than it sounds) and X-23. X-23 and Jubilee◊. And this◊. Nicknamed appropriately, the "vampire Lesbian scene". Although the writers seem to be genre savvy, since they have Jubilee claim she was merely acting under the influence of her vampire instincts...sure.
Truly genre savvy writers would have known that excuse would convince no-one.
Some suspect X-23 had a little unrequited crush on Dust. Look at the lengths she went to in order to keep the bigoted Striker from killing Dust during the Purifiers' post-M Day attack on the school. More recently, when Dust and Laura were reunited in Avengers Academy's "A vs. X" arc, Laura makes an awkward attempt to compliment Dust; throughout the arc, their relationship is one of the side-conflicts that must be resolved.
Her relationship with Academy member Finesse edges this at points, especially as both are unemotionally devoid Bosom Buddies who bond over fighting and analyzing. The relationship goes sour and their final talk in Academy almost reads like a sorrow filled break up, with X-23 walking away from Finesse saying she felt betrayed by her actions.
Kitty Pryde has been mentioned on this page already, but this troper believes special mention must be made of her relationship with Storm. The older woman is the only person in the X-Universe who actually calls her "Kitten" as a term of endearment, and the troper can attest to there being at least one fanfic out there dedicated to Ororo seeing Kitty as more than "the daughter she never had" (which is the type of relationship they share in canon).
Then there's the Mutant X short series where Ororo is a vampire who turns Kitty (and Forge) into her slaves.
In X-Men Unlimited issue 22, Marrow gets downright poetic about Kitty Pryde's loveliness (before throwing a dead rat into her lap.) As a Morlock, it's supposed to be jealousy of/distate for one of the "pretty" mutants who have it so easy, but that comes off as an Informed Attribute as it's very understated and Kitty's beauty and perfection is emphasized a great deal (the entire story is seen through Marrow's eyes.) The entire portion of the issue that isn't devoted to heroing is Marrow acting like a child teasing her crush while thinking about how lovely and perfect Kitty is.
So, in summary, Logan is the person most affected by the death of Nightcrawler, he keeps a photograph of their happy days in his pocket, he said how much he misses him, looks at a photograph of him before heading out on one of his missions with X-Force, and hits Dark Beast for attacking a Kurt alternative. Then he puts Kurt and Jean Grey on the same level, said how much he loves his voice, called AOA! Kurt "elf", without really doing it on purpose and, at an earlier stage, has let his school be invaded by horrible blue dwarfs, only because they vaguely look like Kurt.
Kurt has descended to earth to help Wolverine with his fight against devils. Not protecting Wolverine is not an option.
Psylocke and Fantomex started out as a fairly ordinary relationship - he fell in love with her, they slept together, he got his heart ripped out by a supervillain and died. Of course, this being comics, he came back. But he came back as three people, all of them still in love with her, and one of them a woman.
Notably, each one gained different aspects of his original person, and while Betsy starts to date one, she finds that he's merely an asshole due to only getting the Jerk part of the originals Jerk with a Heart of Gold personality. After they break up, the female Fantomex clone approaches her, and the two quickly realize that the aspects of him that Betsy was in love with were the ones she got. Its at this point its no longer subtext.
Iceman and Beast also get this every now and then.
Scott and Lance. More Ho Yay than their usual Foe Yay when Lance joined the X-Men in one episode.
There are also Kitty and Rogue (and their famous dance scene), Rogue and Jean, and the lesbian orgy that is the "On the Wild Side" montage with Jean and Amara grinding on each other.
Wolverine and Captain America, in a really sweet, sad kinda way.
The first scene Angel and Gambit have together is a shirtless Angel walking in on Gambit, who just broke in to his house, and asking him if he"likes what he sees". Wow...
Then once Angel gets to the Institute, Kitty and Amara are spying on him. Bobby sneaks up behind, asks them if they're "checking him out". Once they leave, he takes their place, even sneaking closer for a better look (my shipping goggle may have been on when I saw this episode though).
"Dark Horizon" had Magneto carrying Xavier around and looking really worried about him. Xavier does not object.
Also in "Dark Horizon", Wolverine and Sabertooth tend to act like a couple who went through a really bad break-up.
Take one good look at the average episode of the '90s cartoon and it's possible to interpret Wolverine as flirting with every male character present, provided you squint a bit in the case of Professor X.
In particular, the animated series created the character of Morph, whose relationship with Wolverine is...noticeably slashy. (Randomly, this caries over and is even surpassed in the comic book adaptation of the show, which simultaneously ups the suggestiveness of their relationship and 'completely removes their friendship. Despite the fact that their deep friendship is needed for Wolverine's behavior to make any level of sense...)
It would be remiss to not mention just how near-canon Rogue/Storm is. Heck, the first time we ever see Rogue's 'dere' side is when she's worrying that Storm's been crushed by debris. We don't see her express that amount of emotional attachment to her canonical love interest Gambit until nearly six episodes later.
Not to mention Magneto. He had a fair number of Foe Yay occasionally bordering on regular Ho Yay moments with Xavier, while his near-infinite patience with Magneto's villainy and the respect the two men hold for one another can't help but remind viewers of similar relationships. Somewhat Hilarious in Hindsight seeing as as several years on, openly gay actor Ian McKellen was cast as Magneto in the live-action films.
Jean: (to Magneto) How much do you love Charles Xavier?
In Wolverine and the X-Men we have scenes of Rogue and Domino hand holding, looking into each other's eyes, and when Rogue goes to rejoin the X-Men... Domino looks like she was about to convince Rogue to stay with the Brotherhood with a kiss...
And as usual Xavier and Magneto have their moments: when Magneto found an injured Xavier unconscious on the shores of Genosha he took Xavier in and put him on life support, looking upon him with great concern when the X-Men caught up with them. Additionally in flashbacks after Magneto cedes defeat to Xavier in allowing a young Jean Grey to stay with Xavier's X-Men, there's a certain suggestiveness to the way they smile and trade barbs with each other after the battle, a certain flirtation almost, if you will, as if between old lovers.
In the First Class movie: Charles and Erik. James McAvoy wasn't kidding when he called it a love story.
In a deleted scene, Charles projects Erik in drag (yes, you read that correctly) and remarks, "You've never looked more beautiful, darling."
Hell, for that matter, James McAvoy and Michael Fassbender. While doing interviews promoting the film they sang to each other and talked about how they would fly all over the world spreading love to the hapless populace if they had super powers. And then there was that time with the golf cart.
Interviewer: What is the most common question you are asked? James McAvoy: How many times did you have sex with Michael Fassbender? Interviewer: That is the question. And what is the answer? McAvoy: Four.
Darwin and Alex (Havoc) have their little moments. There is a scene where Darwin places his hand on Alex's stomach, and just a few seconds before Darwin dies, who does he reach out to? Alex.
Erik tells Emma that he wants her on his team to fill the "gap in [his] life" left by Xavier.
Who, it is important to note, he has know for a few weeks tops.
There's such a ridiculous amount of Ho Yay in this movie, that by the end it almost feels like Charles is cheating on Erik when he kisses Moira. Certainly the fact that Erik was absolutely devoted to turning those missiles on the Russians and Americans and the only thing that stops him is Charles getting shot, whereupon he falls to his knees in abject horror and forgets the thousands of soldiers just off the coastdoesn't help things! And that's one example.
As blatantly homoerotic as the entire film is, the scene where Charles reads Erik's mind and then wipes away a tear takes the cake.
Erik: What did you do to me?
Charles: I accessed the brightest corner of your memory system. It's a very beautiful memory, Erik. Thank you.
On the villainous side, the Azazel/Riptide pairing is as popular as Azazel/Mystique.
Yes, really. In X-Men Legends II, we've got Brotherhood and X-Men working together, and when Toad talks about how Magneto should be in charge and not Xavier, Magneto said "Charles and I discuss everything before a mission." With emphasis on Xavier's name just like that. You'd have to hear it, but the way he said it sounded like the bratty kids preferring one parent's way to the other but the other assures them that all decisions are made as a unit. In general, the bickering between the two teams in almost every cutscene makes Charles and Erik Mommy and Daddy to bickering siblings for the entire game. And nobody but the other calls either by his first name (except Emma Frost at one point.) It probably sounds like a Shipping Goggles-based stretch to anyone who hasn't played it but it's unmistakeable to anyone who has.