Superman had a crossover with Captain Marvel where they bonded over having similar powers and ends with Captain Marvel's friend dying due to a hit squad when he's Billy Batson and then storming the police station the hit squad was in custody at. Superman calls him out on it and then finds out the truth about Captain Marvel being a 10 year old boy. Superman naturally calls out the wizard who gave Billy his powers and identity as Captain Marvel and the wizard asks Superman to help guide him. Clark Kent meets Billy Batson who is living in a rundown building and reveals his secret identity so Billy has someone to count on.
There isn't one interpretation of the Kents' discovery of baby Kal-El that doesn't qualify as a CMOH.
Superman's first meeting with Lois, in Action Comics #1: "You needn't be afraid of me. I won't harm you." Made all the better when Alex Ross painted it.
There's a bit in the Chris Kent storyline in Superman, when Chris and Clark visit the Batcave. Clark's adopted son is impressed, in classic little-boy fashion, by Robin's acrobatics and begs to learn. Keep in mind that this is a kid who can fly. It's just adorable.
Superman: You fight against Joker, against Two-Face, against Catwoman. But this... [Indicates Smallville] This is what I fight for.
During the "Funeral For a Friend" storyline in the early 90's, Ma and Pa Kent are unable to attend Superman's funeral in Metropolis, so to say goodbye to their son, they bury a box containing items from his childhood (including a blanket and a teddy bear) in the crater made by his spaceship.
A lot of "Funeral For a Friend" was full of Tear Jerkers and CMOHs, but I found the related subtle Red Skies Crossovers in the other titles to be even more heartwarming — the death of Superman was such a huge loss that it was basically treated like a Crisis Crossover. Special props to a moment from Batman during the nightmarish lead up to the Knightfall event, where a morbidly depressed Bruce Wayne wallows in despair in the cave, and it's revealed that he's still wearing one of the JLA's Superman-Shield black armbands, reminding the reader just how miserable and hopeless Bruce's world is right now. Because he can't even call up Clark to help him, either with his problems or with emotional support, just when he most needed it. Awww...
Let's face it, the entire point of "Funeral For a Friend" was to show how much Superman was loved by the entire planet and a great tribute to the character.
By the end of The Death of Superman, Lois Lane is an emotional wreck. She's gone through the trauma of Clark dying in her arms, has had to deal with his four would-be heirs, and even when the real Superman initially comes back she won't allow herself to believe him despite some very compelling (and very personal) evidence. After Supes takes down the Big Bad with a little help from his friends, we cut to Lois in her apartment, lying in bed fully clothed in the middle of the afternoon, possibly hung over. She hears a tapping on her window and assumes it's a bird, a call back to a scene much earlier in the arc. She flings open the drapes to reveal a great big "S." The next scene is a full-page panel of Lois and Superman kissing in midair. Text reads, "There isn't a doubt in her mind. She's in his arms... faster than a speeding bullet."
The issue after that shows Superman rescuing a young boy and girl (presumably brother and sister) from a disused Civil Defense shelter where they've been trapped since the battle with Doomsday, a couple of months at least. The kids have been living on the food and water supplies they found - they're malnourished and dehydrated, but they're alive. The little girl tells Big Blue that she kept reassuring her brother that no matter how long it took, Superman would eventually come and get them - he wouldn't let them die. Superman replies that he would rather die himself. And we believe him, because he did.
There's a Superman arc wherein we gain a glimpse into Krypto the Superdog's thought processes (which are mostly along the line of "Manthrow stick! Krypto get stick! Make Man happy!"). During this arc, the supervillain Atlas, backed by a secret group within the United States military, has all but defeated Superman and his allies in battle... until Krypto appears, and he's not happy. He withstands both Atlas' strength and the weaponry of the military to fight Atlas and buy Superman some time, all out of loyalty to Superman. Then, when Atlas is dealt with, Superman delivers a speech about how Krypto isn't just his dog, but belongs to Metropolis — and as the city celebrates Krypto and his master pets him, we get this thought from Krypto.
I am heartwarmed anew every single time someone tries to induce a Heroic BSOD on Superman. It never works, but seeing Superman demonstrate just why he's Earth's greatest hero always brightens my day.
Near the end of JLA/Hitman #2, when Superman flies up above the atmosphere to gaze down at the Earth, musing about its beauty and his landing there as an infant. He pauses, deep in thought, and then:
No line before or since has more simply and vividly captured just how insanely much Clark Kent loves his adopted planet.
In the issue where the Eradicator Program's manifestation of Kem-L accosts Clark in his apartment and tries to "disinfect" him of human influence, telling him to leave Earth and embrace his Kryptonian heritage, arguing that humans are unworthy for a race as superior to them as Kryptonians to live with and constantly calling him "Kal-El". Clark's counterargument is rather simple:
"My name is Clark Kent. Get out of my home. Get off my planet."
In a 90s Superman Christmas issue, Lois asked Superman if he would be willing to put in an appearance at the Daily Planet's annual charity Christmas party for a Metropolis foster care center, to take the kids' minds off the fact that the Planet couldn't afford to buy toys for the kids due to budget cuts (Metropolis had been nearly leveled by Lex Luthor in an earlier arc). Superman had a better idea: he convinced Professor Emil Hamilton (this was years before his most recent Face-Heel Turn) to dress as Santa Claus and cobble together a quick sleigh, borrowed some reindeer from the Metropolis Zoo, and called up a friend of his in Gotham City, who was happy to contact a Metropolis toy-store for toys and have them give him the bill. Superman, in a solid black body-stocking so he wouldn't be noticed in the night sky, carried the sleigh and reindeer to the Daily Planet roof, where Professor Hamilton gleefully distributed the toys.
During the Brainiac arc, just before Superman flies off to track down Brainiac he has a chat with Pa Kent. Pa shows Clark a whole bunch of mementos from Clark's childhood (such as a baseball Clark knocked clear across Smallville). Now, this is heartwarming enough on its own, but what clinches it is Clark engraving World's Greatest Dad on a horseshoe and giving it to his adoptive father before he goes.
Which makes Pa's death at the end even more of a Tear Jerker.
The last issue of the Superman titles before the FlashpointContinuity Reboot. It gives distant finales to most of the comic's loose ends, and then assures us that, in that timeline at least, Superman and Lois stayed married and got to live happily ever after.
The original Lexor story by Otto Binder, when Lex passes up a chance to defeat Superman in order to help a dying civilization (well, at least to get out of the way and let Superman help them). The Lexorians hail Lex as a hero.
The time travel story when Luthor gets into a fight with Superboy in the nineteenth century, and realizes too late that he's accidentally prevented him from stopping John Wilkes Booth—making Lex indirectly responsible for the death of Lincoln. He's aghast, and leaves Superboy alone and returns to the present, badly shaken.
In "The Galactic Golem," Lex believes he's accidentally wiped out all of humanity when a scheme of his went out of control, leaving him the last man on Earth. He's horrified. When he learns everybody's fine (of course Superman saved the day), he stretches out his arms to take in the beautiful sight of ordinary people going about their business, overwhelmingly relieved, and says he doesn't even mind Superman carting him off to jail, as long as everyone's okay.
In a What If? story, a D-list villain has killed Lois, and then returns to further torment Superman while he's grieving. Luthor and Brainiac show up to catch the villain and hand him over to Supes, saying when all's said and done, they respect him too much to watch what this scum was doing to him.
"The Einstein Connection,'' when Superman realizes that Lex's hero is Albert Einstein. Lex passes up a chance to escape so he can rescue a drowning child—because he just can't bring himself to be a Jerk Ass on Einstein's birthday. Instead of taking him straight back to jail, Supes flies him to the Smithsonian's Einstein exhibit — a place Lex has always wanted to go, but never could because it's so public, and he's a wanted man. Deeply moved, he looks up at the Einstein statue and says, quietly, "Happy birthday, sir." When Superman finally does take Lex back to prison, Lex says, "Thanks for everything."
Superman: If you honestly believe in your heart of hearts, that you will never ever have another happy day ó then step out into the air. Iíll keep my promise. I wonít stop you. But if you think thereís a chance no matter how small ó that there might be just one more happy day out there ó then Take My Hand.
Not seen so much any more, but it used to be a stock ending in Superman stories to see Clark back at the office with his friends, after the day has been saved and the world is safe again. Lois or someone would say something unintentionally lampshading Clark's secret identity, and he would turn to the reader, smile, and wink. Maybe it's corny, but it feels good every single time.
The scene where Jor-El and Lara prepare to send their little boy off to Earth. The music, the dialogue, even the costumes and sets. I mean... damn. But even before that...
Lara: He'll be isolated. Different... Alone.
Jor-El: (takes a deep breath, and holds up a single green crystal) He will not be alone. He will never be alone.
When Clark first meets Jor-El and begins his training. Under the tutelage of his father's watchful eye Earth's greatest hero begins his training.
Jor-El: ...they can be a great people, Kal-El; they wish to be. They only lack the light to show them the way. For this reason above all, their capacity for good, I have sent them you: my only son.
The conversation between Superman and Jor-El after Superman's first night as a superhero in the extended cut of Superman: The Movie. Numerous examples in Superman Returns, a rare 21st century film that is unapologetically sentimental and free of cynicism.
Clark's last heart to heart talk with Pa Kent before he dies.
Pa Kent:"There's one thing that I do know for sure, son. And that is, you are here for a reason."
The scene of young Clark telling Ma Kent he has to leave Kansas while standing in the majestic waves of grain.
The scene where Clark Kent tells Mr. White to arrange for half his salary to go to his Mom back home. Even the jaded Lois is impressed.
Clark: Uh, Mr White, I'd be grateful if you could arrange for half my salary to go to this address on a weekly basis?
Lois: Your bookie, right?
Lois: Don't tell me — he gives his money to his sweet grey haired old mother.
Clark: Actually, she's silver-haired.
Perry White: (snatches the address wearing a look of surprise) I'll see what I can do.
Clark: Oh, um, uh, thank you very much, um, Mr White.
Superman: Peter Pan, huh? Peter Pan flew with children, Lois. In a fairytale.
Speaking of that entire scene, Lois Lane, hard-bitten reporter, completely fangirling out over Supes. "Do you...like pink?"
The last shot of each of the older films, Christopher Reeve looks at the audience, smiles and flies off, giving audiences a dose of optimism.
The scene where Kal-El lands on earth there were 2 heartwarming moments on his part. The first thing he does upon meeting Martha Kent is hug her affectionately. Whilst the second which becomes a Wham Episode for them, is when he stops the car from crushing Johnathan. It goes to show that even as a kid, not all his kindness came from their influence. It also gives this troper the impression, that they didn't find the soon to be Clark Kent. He found them.
Just for fun, Elliot S! Maggin wrote a prose short story called Starwinds Howl about all the adventures Krypto the Superdog had in space before coming to Earth. As it should be, the story is told absolutely straight—from Krpyto's point of view, and without depicting his thoughts as speech. The scene at the end, when Superboy is unexpectedly reunited with his childhood pet, is wonderful.