Brace yourselves... There's ONE - count it, one - example in the Warhammer 40,000 universe. After the Administratum decided that killing off an entire world would be preferable to risking that any of the survivors might fall to Chaos - which was unlikely, considering that they'd just won a major war against Chaos - Logan Grimnar, the Chapter Master of the Space Wolves, stood up and called them out on their shit. To put this in perspective, anyone else even questioning the Imperium's methods is almost always killed messily. Logan stood up for what was right, told them that they were wrong and that he'd never forgive them. The fact that he managed to get away with it is a CMOA itself, but the fact that someone in the galaxy isn't a horrible bloodthirsty monster is downright heartwarming, considering the setting.
Even better- the Space Wolves are a bunch of bloodthirsty Super Soldiers from a Death World, who'll destroy whole cities if they have to, and Logan would be a paragon of everything they stand for- and he's standing up for innocent human lives. The Space Marines were made to unite and defend humanity- the Space Wolves may be among the few who remember that.
This may partially be because of Bjorn the Fell-Handed, who is probably the oldest Space Marine Dreadnaught still in service, and indeed, the oldest known warrior still in service to the Empire. He is so old, he even fought alongside Leman Russ and the Emperor themselves during the Horus heresy, and also became the Space Wolves' first chapter master after Leman Russ dissapeared. It is highly likely that he has passed on knowledge from back then.
One thing that should be noted is that a lot of the Heart Warming moments in 40k come from the Black Library books (which are all of arguable canon). The Space Wolves one is straight fluff, from an article about their Chapter Master.
Actually, there's plenty of CMOHs in Warhammer 40,000 - its crapsacky setting actually lends itself to them. Admittedly, this usually involves the Imperial Guard - your average Guardsman is just an average human being caught in one of the worst settings imaginable. Look at any number of the Imperial Guard novels, and even some of the Space Marine ones - particularly the Ultramarines. The Space Wolves certainly don't have a monopoly on - shock! concern for people's lives, as Captain Uriel Ventris of the Ultramarines or Captain Elaric Eshara of the Imperial Fists will tell you.
The SoulDrinkers series. Emperor's bowels, the Soul Drinkers series. Despite the main characters' name and their mutations. One Marine realises he regrets the death of a Guardsman now that he's forced by circumstances into killing them himself rather than simply sending them to their deaths. An aging Imperial Guard general who's spent most of the time sitting in a Baneblade realises the planet is lost and decides to die with his men rather than escape. Sarpedon refuses to attack major Imperial military centres even though everyone is busy at the Eye of Terror, because he knows that for all its ruthless crushing tyranny it's still the only thing protecting people from Chaos. And the author states that even if Sarpedon's ideals lead to his Chapter's annihilation (it's come pretty close at least four times in five books), at least they will die free.
The soul drinkers left the imperium, subjected themselves to being attacked by almost everyone, and waged a personal war ON said imperium, because they believe that they are going the wrong way about things. Which, almost certainly, they are. This is a group of rapidly dwindling, mutation ravaged survivors, fighting for what they believe in.
Arguably, Lord Castellan Usarker E. Creed is one. He values a soldiers life far more than an ordinary commander, even doing so much as suspending summary executions within his regiment. The Codex even says he is intensely disliked by the Commissars.
Salamanders Chapter + Planet Armageddon = Instant CMOH. Whether it's stalwartly defending the retreating refugees or moving in to protect hives that have been left to be wiped out by the Orks. Best of all, it's rumoured that Chapter Master Tu'shan beat up a Captain in the Marines Malevolent for bombarding a refugee camp because Orks had breached the perimeter. Were it not for the Orks being involved, one could forget that it was Warhammer40000 at all.
A... Naturally twisted and arguable one comes from the depths of Chaos itself, the faction of Chaotic Evil, the chief enemy of all sentient life. Those who know of Nurgle, the god of disease and decay, know that despite the intense pain he causes, he and his followers are known to be on a slightly disturbing level of Affably Evil. One instance stands out though. During the Fall of the Eldar, as gods were being snapped up left and right by Slaanesh, Nurgle happened to take notice of Isha, the goddess of life. With speed uncharacteristic of the God of Decay, he launched a war to save her in time. No other Chaos god has shown the capacity to actually rescue someone. Of course, the twisted part of having rescued and sequestered her in his gardens is that his way of showing affection is decidedly... unpleasant. It goes back into fuzz, however, in that he lets her develop and give out cures for his diseases. That's right, he lets her thwart him. With no real motive beyond trying to be nice. Like I said, twisted
Nurgle is outright stated to be a very fatherly and loving fellow. The only reason he's even considered evil is because he thinks illness and disease are literally what everyone wants, and that your suffering at said diseases are thank yous. If he knew that wasn't the case, he'd probably be quite the nice guy.
Allow me to explain the Heartwarming Moments involving Space Marines for the uninitiated. Space Marines are 9 foot tall walking tanks who can spit acid, breath in almost any toxin known and punch holes through a man's chest. They are taken when they are early teens (or earlier!) from, usually, the worst civilizations in the galaxy, places where most men die before they hit puberty. They are brainwashed into remorseless killing machines, monsters taught that the lives of a million ordinary men aren't worth theirs, that they must survive and kill any and all aliens, mutants and heretics (even though by the standards the Imperium holds they basically are all 3 of these)... and yet 99% of them will still stand up, flip off any and all Imperial organisations that threaten the Imperial Guard.
The story's also related on the Off the Rails page. Apparently, the Game Master tried to give a party some kind of moral test by leaving two very powerful objects guarded by a tiny little girl (who wasn't real, and could only say "No" and "Please do not take these items".) Instead of doing anything simple, the party assumed the girl had been traumatized and spent ages trying to get her to snap out of it, sweet in itself. Eventually, the party's bard played a song for her to try and help, and because he rolled well, the GM let her Cry Cute very, very slightly. The party's response? They decided she was the cutest, most Moe thing ever and decided to take her with them. Eventually the GM gave into the cute and let her develop a mind. She became the group's mascot, Noh. Say it with me: awwwwww!
The Book of Exalted Deeds, a work which sets up its basecamp on the far Idealism end of the Sliding Scale of Idealism Versus Cynicism, and actually makes it work. The main cause: it stated no-one is beyond redemption, not even members of Always Chaotic Evil races (well, except demons and devils, but since they're made from evil, that really isn't too much of a surprise). They demonstrated this by having a sample character who was a reformed mind flayer. The idea of a creature that pretty much defines Lawful Evil, can only survive on brains, and comes from a culture based on telepathic slavery, learning that there is a better way and ending up on the side of light...
Even more so the idea of redeeming evil items. The fact that someone somewhere made an armor made solely to allow only the most evil bastards to resemble a demon, and even that armor can be taught the ways of good...it's just...wow!
The Apostle of Peace. The entire point of the class is that, in a gameline where Violence Is The Only Answer more often than not, they exist to say "There are other ways to do this". And prove it.
Rudolph van Richten, Ravenloft's greatest monster-hunter/expert, lost his only child when a tribe of Vistani gypsies sold his kidnapped boy Erasmus to a vampire. In grief-maddened vengeance, he destroyed the entire tribe, save one survivor who'd been away from camp. Decades later, Van Richten and the survivor meet face to face, and manage to set mutual recriminations aside, swearing forgiveness and friendship in a CMOH for the ages.
On the matter of D&D CMOHs, there is about one for every two items in the book Weapons Of Legacy.
Bullybasher's Gauntlets. "... [the hero] used much of his own wealth to finance a hospital for the poor, so poverty would never again make the difference between one of them living or dying." Priceless.
Celdoriath's Clarion. Celdoriath was an Elven ranger who won the right to wed his king's daughter by sheer awesome.
Coral Bite, a trident wielded by Ildashurn, a doppelganger who stole the form of an aquatic elf, Sajolveun, that he killed by mistake : "Feeling guilty, the doppelganger studied the elf's life from his underwater home, adopted Sajolveun's identity, and returned to the aquatic elves. Ildashurn did everything in his power to amend the mistake he had made. In so doing, however, he fell in love with the aquatic elves and became their hero. Even his legendary weapon had embraced him completely. When Ildashurn could no longer politely avoid the topic of marriage, he announced that he would be leaving to fulfill a personal quest, promising to take a wife upon his return. Privately, Ildashurn had no intention of returning. When he reached the surface and tried changing back into an air-breathing creature, the doppelganger discovered that he could not. He was no longer a shapechanger. Somehow, he had become an aquatic elf. Perhaps it was some strange effect of his trident's power, or perhaps it was the act of some benevolent deity. Ildashurn didn't care. He just smiled and dove back into the water."
Divine Spark, a Holy Symbol used to unite all the religions against the enemies of life.
... and more. The paladin's ghost that lingers to finish the training of his apprentice, who turns and just smiles at him; at that, the spirit passes on. The other paladin soul, captured in an über-evil blade, that ends up redeeming it. The messenger who seeks the god of travel to give his successor abilities to match his own, so that he not be mocked for not living up to an impossible legacy. And so on and so forth.
The Deadlands rulebook Fire and Brimstone, which is about the Blessed, who use powers from God. It is perhaps the penultimate tabletop RPG example of the trope God Is Good, for it has some amazing spells in it. A personal favorite is Untouchable... for three rounds, nothing on earth can harm you. What does the example player use this power for? He's going to kick some bad guy's ass from here to Texas, right? No. He does something more heroic with it. He uses the power to save a little girl from a burning house.
There's also an ability that makes a person feel terrible for lying, cheating, or generally being bad. No game effects, but it makes them feel... bad. Used cleverly, it's responsible for more Heel Face Turns than all the other miracles put together.
And if you ever wonder if a Promethean's pilgrimage is really worth it, there's this little story at the end of a chapter about a driver who casually, and just because he wants to help, picks up a battered and confused man to lead him to the hospital, not understanding why the man seems so baffled by this act of generosity. It's pretty clear he actually picked up a Promethean who finally managed to reach the New Dawn and to become a real human. The story ends with the driver looking in his rear mirror only for seeing the man smiling and opening his arms for welcoming the rays of the sun.
Hunter: The Vigil, too. Sure, it's dark and depressing, but the message of this game is simple: the reason humanity hasn't fallen to the countless horrors of the universe over the centuries, the reason ordinary people sleep soundly in their beds, the reason the protagonists of the other game lines (with a couple of exceptions, like Promethean and Geist) will NEVER win is because ordinary men and women step into the darkness and take up the Vigil. Many go insane. Most die. But for every candle that goes out, another ignites and the Vigil remains.
Changeling: The Lost too. Yes, You've been traumatized by horrible things. Yes, you're living a life that may potentially lead to one of multiple horror filled and nightmarish ends. But even in Changeling, there is hope that one day, you can reunite with your fetch peacefully and regain wholeness, or come to grips with your powers without descending into Madness. The hope may be small, but if the appearance of the Court of the Dawn (The Court powered by the emotion of HOPE) is symbolic of anything, its that even for the Lost, hope can burn brightly and powerfully enough to give a chance for a better tommorow.
The origin of the Monkey Clan in Legend of the Five Rings. During a war against the Shadowlands, a samurai named Toku emerged as a hero. Emperor Toturi I asked Toku to serve as the Captain of the Imperial Guard... and he turned the offer down. The reason? He wasn't a samurai at all - his village was attacked, and he'd stolen the swords off a dead samurai's body to defend it. Then he headed out to join the battle, promising himself he'd make up for his crimes after it was over. The confession complete, he asked to be allowed to commit seppuku... and was refused. The emperor told Toku he'd done more to earn his rank than any of the born samurai in Rokugan, and offically made Toku a samurai, retroactive to the beginning of the war. Then he ordered Toku to be the head of the newly-formed Monkey Clan as well as Captain of the Guard. The Monkey Clan is quite possibly the most respected Minor Clan in Rokugan.
Actually playing the L 5 R tabletop game ends itself to this naturally. In one game I G Med, a Moto Berserker, had just seen the Dragon clan magistrate he was in love with die in a war that Moto Chagatai, the Berserker's own lord, caused out of greed and naked ambition. The Berserker immediately heeled his horse around, and charged his own lord and his lord's personal guard. I told the player, "You know that's suicide right? You're not even going to get close enough to scuff Chagatai's armour." The player's response? "I know."
My other story involves a plot to assassinate the Empress by the Scorpion clan. At the time, the PCs were playing the Empress' guard, fleeing a burning castle that had been attacked en masse by ninja. The one Hida Bushi player, having already been hobbled by a poison arrow, gets a weird look on his face and tells the GM, "My character stops and turns around, spits on his hands and lifts his ono in a fighting stance." It took an ever-escalating combat involving some eighteen ninjas to take the Hida down for good, and that character's last act was to make a called shot for the ninja commander's face that shattered the commander's face mask and left an ugly scar for the rest of the campaign.
To put this in clearer perspective, the Monkey Clan was given their lands from those of the notoriously underhanded Scorpion Clan, a clan that openly celebrates blackmail, poison, and Disproportionate Retribution. And they have sworn the last on any who touch the Monkey Clan.
FATAL has the Flute of Felicity, aka "What The Hell Is A Flute That Makes People Happy Doing In A Piece Of Shit World Like FATAL"? (On the forum thread, at least two tropers attempted to "rescue" the Flute of Felicity from the tainted mires of its source material.)
Neverwinter Nights persistant world... but it's faithful to DnD, so it mostly applies here: My character, Nashanee, is a Tiefling (a part fiend) came to the City of Sharressia because she really couldn't fit in anywhere else, being hated for her fiendish heritage. After several months, and a few relationships ranging from the casual to the heartbreaking, she finally gets into one that is going very well with a Half-Dragon woman named Kalia. After a while, they get serious with eachother, and in a moment that is this trope in and of itself they essentially propose to one another (though they can't marry). Later, while performing... *ahem* activities in the temple, with Nash sitting on the Alter, Kalia kneels to Nashanee, and when inquired as too why, responds, "Because you're supposed to kneel before the Divine, and that is what you are." To anyone else, it might have been pleasantly corny, but spoken to a quarter fiend who had spent her life suffering because of how she decidedly wasn't divine, it was a truly touching thing to say.
In GurpsTravellerSword Worlds, there is a CMOH in the side notes. A Sword World soldier is slogging home after the Fifth Frontier War. When he arrives he sees his home is in ruins, but there is his wife gallantly putting the pieces of their home together. They greet each other and the next day get back to work rebuilding their lives and proving that their spirits are unbreakable. Later the soldier meets his brother who wishes to go on an expedition to the back of beyond to escape the encroachments of the Imperium. The soldier then says that he wishes his brother good luck but for himself, his home is right where it is and There's No Place Like Home.
One major antagonist in our game of Scion was a Scion of Loki, a teen runaway and con artist with a bit of a thing for our heroine. She was also a complete and utter Daddy's Girl, with a far better relationship with Loki than any of the PCs had with their divine parents. The relationship didn't show up much, but when it did it was pretty much always one of these.
One example of this, mixed with Tear Jerker and Crowning Moment Of Awesome, happened towards the end of the game, when Loki was bound with the entrails of his son and abandoned in the bowels of the earth with Sigyn. The aforementioned Scion (by this point god-level) spent years manipulating her way into Odin's good graces, becoming indispensable to him and generally going against everything she stood for...in order to stab Odin in the back at just the right moment, take control of the apples of Idunn and take over Asgard, so she could bring her father and stepmother home. It didn't last long, of course, as the PCs were loyal to Odin and eventually won, but the levelofdevotion the girl displayed throughout was incredible, and all the sweeter for being very clearly reciprocated.
In a game of Pathfinder, we were heading towards a goblin cavern. When we got there, we found a leopard. She was very pregnant, very hurt, and starving. The goblins had apparently captured her and forced her to guard the entrance to their cave. Outraged at this act of cruelty, the party ranger set about setting the leopard free. The party Rogue, who was a classic Chaotic Neutral mercenary type, was so outraged himself that he volunteered a healing potion to the leopard if it meant healing her. The leopard went into labor as he was doing so, and the player ended up using his ranks in the Heal skill to try to save the cubs and the mother. The last one was the runt and nearly dead, but the ranger managed to save her life. The party interrupted the game to make sure the leopard mother and her cubs were put in a safe place. A few months in-game later, the ranger discovered that the cub, now nearly full-grown, was following him, he had his animal companion.
I'm currently DMing a Dungeons and Dragons campaign where the final villains are a human half-fiend fighter and his lich half-brother. The pair are collecting fragments of a sword that the last time it was used helped simultaneously destroy and rebuild the world (it's complicated). The thing is, they don't want to use it to take over the world or anything like that. What they want is to reforge it and take it to the tomb of the sword's original owner: their father. The event that shattered the sword also completely destroyed his body, so the two are trying to get the one thing they could possibly have left in his memory.
Rather surprisingly, there's one in Ninja Burger. One of the delivery cards the players can draw is to deliver a tasty Ninja Burger meal to a firefighter while he's in the middle of fighting a fire. One of the rolls is a Combat roll. Why? Because as the card says, "It is an honor to aid these warriors against their foe."