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Wolverine: Just remember. I'm still the most screwed up person in the universe.
Marvel Adventures: Iron Man had one issue where a kid falls into a hole in a field in the middle of Nebraska. Since it's old Stark-tech property, Tony Stark comes down, as Iron Man, to rescue the kid. Turns out it a nuke-proof bunker built by his father, Harold, to preserve something. At one point Tony thinks about how his dad was so remote. Later on he fights some Zeerust robots, who stop fighting when he tells them he's "Designate: Stark, Anthony", and open the vault. Tony is stunned by what he sees in there before turning to leave. The last panel of the comic shows us the contents; pictures of Tony at all the events Howard could never make it to. This is what he chose to survive a nuclear apocalypse. It's a cliché, but still aww-worthy.
The idea that Steve Rogers is in the Marvel Adventures universe right now is a CMOH for me.
Of all people, Norman Osborn gets one in Dark Avengers, where he has a talk with the Sentry, who has a Superpowered Evil Side know as the Void. For the most part, everyone else helps him by fighting the Void, Osborn, on the other hand, tells him that he knows what's it like to have a evil side and that there is no Void, it's just the results of the Sentry refusing to embrace his human side (as he doesn't sleep or eat anymore), then takes him out for a hamburger.
The Avengers #57 when the android Vision is accepted into the team.
Henry Pym: Is a man any less human because he has an artificial leg... or a transplanted heart? The five original Avengers included an Asgardian immortal... And a green-skinned tormented behemoth! We ask merely a man's worth... not the accident of his condition!
(Vision excuses himself, goes into the next room and cries in a very human manner.)
In an issue of Marvel Adventures: Fantastic Four, Sue has felt increasingly ignored and sidelined by her team mates, to the extent that she's thinking of leaving them to join S.H.I.E.L.D and work with Nick Fury. Then, as she's working up the courage to tell them she's leaving, they are distracted by an interview they did after an earlier battle... in which all three of her friends cheerfully admit that Sue's the strength behind them and that they'd be lost and useless without her. And what makes it especially genuine — and thus the more heartwarming — is that none of the other members are even aware that she's been working for S.H.I.E.L.D on the side, much less thinking of leaving.
In another issue we see a future version of Galactus observing the present day FF before he plans to exit the dying universe for the next one, he then brings the FF to his time to fight off four villains trying to stop him from leaving. In the end Galactus shows that the villains were no threat to him, and Reed deduces the reals reason Galactus had summoned them; he was lonely and wanted someone to say spend time with before the universe ended.
Although the Secret Invasion ends sadly, there is one heartwarming moment: Spider Woman was impersonated by the Skrull Queen and was just rescued. Unfortunately, most heroes have grown so accustomed by the Skrull Queen using her guise so they look at her full of suspicion. Ms. Marvel was the only one who genuinely approached her... and hugged her out of relief, as in their friendship didn't get strained even if she was interacting with an imposter all the time. And this is coming from one of the heroines who kicked dogs with Iron Man in Civil War!
Another one from Secret Invasion is Clint being reunited with the real Bobbi Morse. After everything that's happened, her death (although not really hers), his death and resurrection, it's a moment of happiness for them both.
In a What If?? story where Captain America isn't revived until the 1980s, and in the meantime an imposter Cap has turned America into a fascist police state, he has a Crowning Moment of Awesome kicking the imposter's ass on live national television. Then he turns to the cameras, berating the people who allowed their blind hero worship to turn their country into the kind of thing Captain America was created to fight. However, he still believes it's possible to return America to the way it was, and the choice is theirs. A murmur flows through the crowd, and after a couple minutes Cap recognizes it: America the Beautiful. At this, he starts crying.
In Alias, after Jessica Jones risks her life investigating a smear campaign against Captain America, Cap comes by in person to collect the tape that would have tied him to a murder case. He asks Jessica why she quit being a superhero, to which she replies that she didn't have what it takes. Cap counters:
"I've met a million people in my life. And I honestly can't think of three who would have done this for me.... So, what I'm saying is, maybe you're being a little hard on yourself."
You wouldn't expect the Punisher to have many of these, and he really doesn't. One, however, comes at the end of "Welcome Back, Frank", the first canon Punisher comic that Garth Ennis wrote for Marvel. Castle is living in a rundown apartment complex with three oddball neighbors: the enthusiastic punk weirdo "Spacker" Dave, the cheerfully obese Mr. Bumpo, and the meek and timid Joan. As he starts becoming familiar with them, he decides it's time to finish up his current mission and move on—only to be shot six times in the chest by an unexpected attack force of mafia soldiers. Dave and Joan find him bleeding out in his apartment and call a mob doctor known for keeping his mouth shut to help the Punisher, and while he's healing he and Joan talk about life. Joan admits that she's terrified of New York City, but can't leave. Frank doesn't believe it, and tells her it's as simple as "Just go[ing]." After he heals and takes out the mob boss, he finds a million dollars in her house safe...which he splits up three ways and leaves for his neighbors to find, along with a note for Joan that says "Just go." Their reactions, and especially Joan's look of tender joy and gratitude, definitely qualify for this trope.
The scene is repeated, though with less emotion, in the 2004Punisher movie.
The reason the movie fails with this is the fact that in comics we see small interactions between the Punisher and his neighbors. When he pulls Bumbo out from door hinges, comments on Dave's new piercings or accepts Joan's bakings. In a story arc about him destroying a mob these moments show us how much he misses being a normal human. He even lampshades this when he is ambushed by the enemy that he "let his guard down" and later when he tells his name to Joan because she deserves to know it. The movie has moments like this but they are more forced and don't feel like part of normal life in the neighborhood.
The Sentry, reviled thoughhe may be, had his own 8-issue miniseries that took place before the current stupidity. He had a psychologist, Dr. Worth, who himself was slowly breaking down under the combined strain of having to keep a frighteningly unstablePhysical God from going nuts and destroying the world and having a miserable home life, with his distant religious fanatic wife Miriam and his crippled, mute daughter Katie. When the Void threatened Dr. Worth, Sentry placed him and his family inside his Watchtower for safekeeping. As Sentry turns to leave, Dr. Worth, his daughter in a chair watching the fireplace, turns to him...
Dr. Worth: Sentry...
Sentry:Please, Cornelius... please don't ask me that. I'm not God. I'd have to do the same for everyone.
Dr. Worth: I would never tell anyone... I promise.
Sentry: I can't.
Dr. Worth: Please, Sentry... I beg of you, please... she's just a child...please...
Seemingly unmoved, Sentry leaves. Dr. Worth slowly walks over to stand behind his daughter's chair, stroking her hair. Then...
Katie:You were in my dream, Daddy.
While Avengers Disassembled is... controversial... it has a very nice heartwarming scene. After Avengers Mansion has been virtually destroyed by an explosion, the paramedics are busy attending to the wounded including the Avengers' loyal butler, Jarvis. Jarvis tries to wave the paramedics on so they can help the other Avengers, but the rather impatient paramedic seems uninterested and callous toward the old man. Then, Captain America himself walks in and berates the medic:
Cap: You will speak to that man, as if you were speaking to me. As far as I'm concerned, that man is an Avenger.
In Avengers Academy, Jennifer Takeda/Hazmat is unable to live outside a special suit or a special room due to her powers constantly making her body generate poison. Hank Pym, aka Giant-Man, promises to find her a cure, and while he hasn't found a permanent one, he does get Leech to come over to nullify Jennifer's powers and let her spend a day as a normal girl. The first thing she does when she comes out of her room is give Hank a hug. It's especially heartwarming considering Hank's nasty reputation as a crazy jerk, so it does a lot to change that perception.
Then, a couple of issues later, the entire Academy is aged up into adult forms in order to fight Korvac. Both Hazmat and Mettle (Who has metal covering his entire body and lacks tactile sensation) discover that in most timelines they are still not able to blend in with society, since Hazmat still has to wear her suit, and Mettle is still, well, metal. The moment in question happens after everyone gets de-aged into their teenage forms (except Reptil, but that's another matter). Mettle comes across Hazmat in the student common room. He asks her if she can take off her helmet, claiming that, being made of metal, her poison won't be able to hurt him. After initially refusing, Hazmat takes off her helmet to reveal that she is crying. This may seem like a Tear Jerker, but what puts it into CMOH territory is that she throws herself into Mettle's arms and Mettle gives us this lovely quote:
Mettle: I know. Me too.
Danny Rand, the Immortal Iron Fist, helping out a bunch of needy kids from Harlem and giving food and blankets to homeless people after turning his entire corporation, Rand Inc., into the largest non-profit charitable organization. You don't see Tony Stark or Bruce Wayne doing that.
Danny: "Come on. Let's see what happens to the world's problems when we throw craploads of money at them."
Bruce Wayne does keep upon his own philanthropy, however seldom mentioned, with his very own Wayne Foundation. Tony Stark, well...
Tony Stark also makes numerous donations to charities, and Stark Industries has an actual foundation—and in a further Crowning Moment of Heartwarming, it's named after his mother, Maria Stark.
At the end of the mini series 1985 it is revealed that the author writes his dead father into the Marvel universe, and getting to know Nurse Jane Foster, who his dad had a crush on. The series is also dedicated to the author's father - double awww.
When he got his own series, Morbius decided to once again try and kill himself. This time however, it appeared that he actually did succeed by forcing himself to not drink any blood. His werewolf friend, Jack Russel, tries to get him to reconsider, but is knocked unconscious by Morbius, who then, so that he does not drink from Jack, stands in front of a window where he allows the sun to burn him. After this, Jack follows through with Morbius's instructions, making his death appear as if he ran him over with his motorcycle. Even though Morbius does not die, it really got to me when Jack tried to find a church that would preside over Morbius's funeral. No one he calls will do it, some even going so far as to condemn Morbius's actions. So, to make up for it, Jack gets some of Morbius's friends together to hold an intimate gathering where they could remember their friend. Even Spider-Man shows up the next day. Though it was after the funeral, it was still very nice to see.