Fluttershy's completely nonjudgemental way of dealing with Fluttercruel. She's scared and upset at first, but then realizes being made by an evil person doesn't make Fluttercruel evil. She promptly agrees to let Fluttercruel stay and promises to help her learn to be a better pony before singing her to sleep. The scene is both awesome and completely adorable at the same time!
The audio adaptation adds extra cuteness to the scene. Fluttercruel's mind scape is depicted in the mirror with her, which is a scary, reflected version of Fluttershy's cottage. When she is sung to sleep, she goes to sleep hugging a sheathed sword, which is strangely adorable.
Also, consider the version of Fluttercruel from the Bad Future. The only words we gets describing her behavior are "You don't want to know what Fluttercruel does." They're just fine telling us the other deeds Discord has done, but apparently Fluttercruel does things so horrible it can't be said. Compare that to the present Fluttercruel, who, while still a bit of a Jerkass, willingly helps Fluttershy talk some sense into Rainbow Dash. It's clear Fluttershy really has made her a better person than she would've been otherwise.
It's revealed when we finally see things from Fluttercruel's perspective that she forced her way into control to help calm down Rainbow Dash. Fluttershy didn't let her out or call her to the surface to do it, she did it all by herself!
When Fluttercruel gains absolute, unrevokable control of their body for a time, she doesn't really do much evil as opposed to being enthralled with singing and walking around on her own terms. Fluttershy might have made the right call on this one.
Rainbow Dash accidentally snaps at Scootaloo and makes her cry. Scootaloo asks if she's going to take her to Cloudsdale to be thrown in the Pegasus Machine and made into rainbow goop. Rainbow Dash replies by revealing to the poor filly it doesn't exist…Then saying even if it did, anyone who tried to get Scootaloo to take her to it would have to go through Rainbow Dash first.
In Rarity's Reharmonizing, Rarity came dangerously close to killing Sweetie Belle accidentally in a fit of rage brought on by her Mind Rape induced phobia of gems and is horrified at how close she came to it. Rarity apologizes to her and tells her she's just ashamed she ever saw a gem as the most beautiful thing in the world. Sweetie Belle asks what is the most beautiful thing in the world to her. This is Rarity's reply:
Rarity: You are, Sweetie; you're the most wonderful and beautiful thing in the world to me. Because you're not a thing. You're my baby sister. There's only one of you. That makes you more precious than a thousand diamonds. And it makes you more special than a million jewels…Jewels can't tell me how much they love me, and they can't listen when I tell them how much I love them. You're the most important thing in the world to me…
It's also a massiveTear Jerker, but Fluttercruel being genuinely concerned for Fluttershy definitely counts!
Applejack Helping everypony, as far as the ones she saw, recover from Discord. Stand outs include:telling Doctor Whooves he's just like everyone else, telling Apple Bloom how brave she was for surviving the events of Story Of The Blanks, giving Rainbow Dash the forgiveness she needed for what happened with Cloudsdale, and telling Derpy and Dinky how strong their bond as mother and daughter is, and that's just for starters…
While admittedly very warped, the fact that Fluttershy is still (technically) just as loving and caring even after her Face-Heel Turn is oddly comforting.
Rarity's entire relationship with Diamond Tiara. Even if Tiara has Fantastic Racism towards unicorns, Rarity takes her under her wing and gets over her phobia of gems to help her make a gift for her mother. She then proceeds to teach her sewing and do everything she can to help her. Even after Diamond Tiara stabs her and runs off, she's got nothing but concern for the poor girl.
It's subtle, but when Pinkie Pie breaks free of Princess Gaia's Lotus-Eater Machine, her Imaginary Friends help her do it. The same ones that we last saw getting murdered by Angry Pie. Pinkie Pie is happy to see them alive again and gives them group hug before leaving, telling them she knows they'll always be with her now. They're imaginary, sure, but it's still touching.
After Trixie is left badly frightened thanks to her crippling fear of Ursas, Pinkie Pie gives her a nuzzle and takes time to calm her down with a rendition of "Giggle At The Ghosties".
While in the Everkind Forest, the group discover the residents of Sunny Town are working for Princess Gaia (it's not revealed rather she broke their curse or not though). Applejack meets Mitta, the pony who had the chance to save Ruby but didn't and was still cursed. Applejack forgives her for what she did and does her best to give her some closure she desperately needs.
However, there's a bit of heartwarming still there because Mitta earned her Cutie Mark before being dragged off, and Fluttershy swears she will return to Sunnytown and help guide them to realizing their wrongdoing and breaking the curse for real.
Seeing the foalified citizens of Ponyville, even Onyx Tiara and Prince Blueblood having fun together and playing in harmony almost makes the reader forget that it's the work of a Mad Goddess.
Don't forget, Celestia herself joined in of her own free will by turning into an Earth Pony filly. Anyone whose seen the series knows how much Celestia wants to have true friendship with her subjects. For just a day, she finally did.
The Mane Cast's group hug following Fluttershy and Pinkie Pie freeing themselves from their curse. Even after all she did, the mane cast will always forgive their friend.
Throughout the story, the Cutie Mark Crusaders try to get through to Silver Spoon and befriend her. During the final chapter, she's the only pony who manages to not only sit through their horrible performance once, but every single time and spends the rest of the celebration with them.
Pinkie: I won't let you walk it alone…Auntie…Auntie Pinkie Pie…will be there for you.
In an alternate universe where Fluttershy and Pinkie Pie didn't let go, the grateful ponies built them a shrine in honor of their sacrifice.
The letter to Celestia at the end of the Princess Gaia Arc, including Trixie and Fluttercruel.
Upon seeing the tortured Fluttershy, Trixie, Twilight and Rarity also notice the Elder Horncalling to them enticingly, each of them able to sense great power within. Despite the promise that this power holds, Twilight effortlessly throws the horn away, focusing instead on helping her friend. None of the unicorns ever give the horn a second thought.
After Fluttercruel is revealed, the Mane Cast, though reasonably surprised at first, have no real problem accepting her as part of the group.
At the end of Pearl Necklace, Princess Celestia revealing how she plans to handle the fallout: by deliberately spreading rumors designed to blame HER for what happened. She knows that some ponies will always believe the worst of her, and willingly exploits that to ensure that Fluttershy's life won't be ruined by her mistakes.
Fluttershy actually sheds Tears of Joy that, after all she's done, Celestia is still willing to do something like this for her.
This is followed by Celestia comforting Twilight, who was nearly heartbroken by the idea of such things being said about her beloved mentor. Celestia hugs her and tells her that no matter what other ponies say about her, Twilight knows what Celestia is really like and that's all that matters. This is enhanced by the fact that about two scenes earlier, Twilight outright states Celestia is like a mother to her, this scene certainly proves it.
After the Elements of Harmony are used to defeat Nightmare Whisper, Fluttercruel appears on the mental plane and begins to fade out of existence. Then, Fluttershy (or at least some part of her) returns, forgives Fluttercruel while acknowledging her own weaknesses, and then saves Fluttercruel — first preventing her destruction and then convincing her that she truly exists as a separate being. Just seeing Fluttershy back to her kind, forgiving self after everything that has happened to her only makes this more heartwarming. They then go off to help the heroes save the rest of Fluttershy.
In the revised version of "Pearl Necklace Part 5", Celestia assumes her Sunny Days disguise and spends the day with Twilight. Knowing how much they both wanted something like this makes it really touching.
Rainbow Dash telling Spitfire that she is a hero, because her and the other Wonderbolts inspire her and others to be heroes. Even after Spitfire keeps telling her how the Wonderbolts aren't heroes, Rainbow doesn't see them as Broken Pedestals and still views them as her heroes.
Luna's second side-story reveals a few things about the Flutters that are touching. They put a necklace of flowers around Discord's statue's neck and spent Hearth's Warming Day in Sunnytown, living up to their word that they would not forsake the cursed ponies. Yes, they forgave Discord!
Pinkie joining the Flutters for their visits to Sunnytown later on, for no other reason than that the cursed ponies are unhappy and that they should be cheered up after all their suffering. She actually gets some of them to laugh for the first time in a millennium and even hugs them despite the fact that it's painful to do so.
Applejack and Orangejack learning that, despite the different choices that they made in life, they are very much the same pony. They quickly forgive what the other thought of them and unite to defeat Nightmare Mirror. Also, when they start to awaken from their vision quest, they each make the other promise to value the ponies most important to them (Applejack's friends and Orangejack's family).
Nurse Redheart's entire POV chapter is pretty much this. She stays in Ponyville as a nurse because she genuinely cares for the ponies in Ponyville like her own family. She could become a doctor, but doesn't because then Mayor Mare couldn't afford to pay her, all because of how much she cares for the townsponies as well as her younger sister.
Nurse Redheart: If I wasn't here, who would be here for these ponies who had been shuffled aside? Ponyville isn't just a collection of houses; it's a family. And it's mine.
At the end of Silver Spoon's day with the Cutie Mark Crusaders, Apple Bloom affirms Spoon's worth as a pony.
Apple Bloom: "Ah realized it on Family Appreciation Day. When yah were the first pony to start clappin' for Granny Smith, even though Diamond Tiara was still tryin' to hurt me an' her. That's when Ah noticed somethin' about yer Cutie Mark Ah hadn't ever noticed before. There's that little heart right there in the handle of it. How you've been actin' today and at the festival just proved it to me. There's a lot more to you and yer Cutie Mark than Ah thought…Maybe the same thing's true about Diamond Tiara…Anyway, goodnight, Silver Spoon."
At the end of the first part of the Mind Games arc, and after an entire chapter of nothing but horrible things happening to her, DiamondTiara is taken by Fancy Pants and Fleur. The simple fact that this is the ONLY good thing to happen to the poor little filly in months is enough for this troper to place it here.
From an officially sanctioned Optional Canon, we get the story of Cadence. Celestia mentions that finding out she was in the universe was "one of the happiest moments of the 1000 years Luna was imprisoned", but what really makes it heartwarming is the letter that Cadence sent to Celestia right after Twilight decided to study friendship in Ponyville.
Cadence: "Dear Aunt Celestia; Zebrafica is lovely this time of year, the diplomatic mission is going well. Thank you for sending Shining Armor to be my bodyguard, it's nice to have a very dear somepony here with me. He's been strangely looking over his shoulder lately but won't tell me why. Do you know? I hear Twilight is staying in Ponyville, that you've given her an assignment studying friendship. To think, that little filly saved the entire world, I'm so proud of her…Twilight studying friendship, are you sure she needs to study it? When I was little, when I didn't have anyone I really connected to except you and my parents…She was the first one I really clicked with. That I really came to think of as my friend. I think she was the one who taught me an important lesson; how it feels to actually form a real friendship…And that's a lesson I use a lot out here on this trips, forming friendships between Equestria and these other places…I owe Twilight a lot… Love, Princess Cadence'."
And afterwards we see that Twilight is crying Tears of joy at hearing such warm words, making it even more beautiful.
There's also the very touching lullaby Celestia sings to her resurrected little sister, and Luna's tears of joy upon meeting Cadence and realizing that she and Celly aren't alone anymore.
Shady: Line of Fate has several, even if it's an Alternate Timeline. A big one being that Luna manages to pull Shady into Good!Discord's nightmare, giving him the resolve to destroy Evil!Discord's spirit instead of being consumed by him, but the big one comes later. Discord, having Evil!Discord's memories, tries to turn himself to stone with the help of a Cockatrice to protect his friends from himself. Shady, however, comes and consoles him. She listens to everything he did before coming to Equestria, all the horrible, monstrous things he did. Discord is sure she'll hate him for it... but she doesn't. She still loves him and accepts him as her son.
Shady: Always remember that you are my son. Nopony can change this, not even Entropy.
As an added bonus Luna and Celestia get to keep their memories and Galaxia doesn't die.
Mind Games part 5 has a flashback to Shady comforting young Discord after a nightmare, and then them having a conversation about what love is. It's made very clear just how much they cared about each other... unfortunately, that just makes what we know came later more of a Tear Jerker.
This chapter also has another Rarity interview, wherein she admits to not thinking she really qualifies as Fluttershy's best friend, only for the Interviewers to empathically assure her that yes she is, reminding her of all she's done to help pull Fluttershy out of her shell.
The following chapter has Spike and Silver Spoon bonding while star gazing.
Rainbow Dash and Scootaloo comforting each other after a shared nightmare (actually a vision of the Epilogue timeline).
The theme song for Reharmonized Ponies, We'll Make It Through. Not only is it just a very uplifting song, there's just something touching about the entire mane cast singing it together, including Trixie and Fluttercruel.
Coffee Swirl manages one in his fifth story; calling the three interviewers his friends despite knowing they're something other than ponies and hugging the Earth Pony interviewer because she hadn't gotten one in any of the canon stories.
Liarjack tricked the Sea Ponies into performing "Modern Major Evil Overlord", to spare Traitor Dash from having to watch the play written about her killing Scootaloo again. Considering Traitor Dash is by this point a broken, tortured, self-loathing wreck, the fact the play actually makes her happy for just a little bit is extremely touching.
While also a BIG Tear Jerker, Liarjack's scene with Epilogue!Apple Bloom is extremely touching. Not only did Apple Bloom manage to break the curse on Sunnytown, she's had a family, but now needs Liarjack to break her curse so she can pass on to join them…and she does.
Liarjack: "…And, yer still mah little sistah, and ah still love ya more than anything, Ah'm dang proud of everythin' ya've done. All yer sins are forgivin', let go of yer guilt, yer free, lay down and get some rest."
Even when she's dying, Cadence in the epilogue world gets one. Despite all the despair she had to protect her changeling people from, despite all the horrors of fighting the Chaos 6, despite Twilight's own despair at seeing Cadence killed right in front of her, her last words to the former elements are: "I forgive..."
Not to mention Cadence managed to redeem the Changelings! Simply by loving them.
The flashback to Shining Armor saying goodbye to Twilight before she leaves for Ponyville and he leaves on Cadence's world tour.
Party at Canterlot Castle. After 1000 years stewing in darkness and trying to hide her heart, the epilogue Twilight Sparkle, thanks to Apple Pie, manages to undergo reharmonization.
Better? Cadence's spirit returns to help her do it, not only hugging her but genuinely forgiving her for her sins.
Apple Tree. Like above, after 1000 years lying with little understanding of why she was doing it really, the epilogue Applejack, thanks to Apple Bloom and the father of Alicorns, not only undergoes reharmonization, but like her Reharmonized counterpart, begins to understand how truth and lies can be used differently. It pulls her out of her self-deception, but also gives her a more proper element: kindness.
Also, think about it. Apple Bloom had one regret when she died, she hadn't healed Applejack's heart and redeemed her. Five hundred years later, she succeeds. And Applejack promises her that some day, she'll earn her way into Pony Heaven to join her.
Another one from that chapter — when Liarjack looks into the Truth, we get another glimpse of Not One Of A Kind, which shows Canon!Discord and his Fluttercruel bonding, and commenting on how it really does feel good to do good.
When aliens invade, Epilogue!Discord travels to the heart of the alien empire to punch their leader in the face…only to find a sick old man on life support. Discord is filled with pity at the sight and gives the man a day of perfect health.
Twilight and Applejack have a proper "waking up" reunion. Even though they weren't strictly what they were looking for, they needed it to remind themselves that they can have old friends again.
The best part is how it subverts what many probably thought would happen. They don't get into a big fight, they realize the other has changed from their Discorded self and sit down and talk things out.
Somewhat disturbing at times, but it's still pretty heartwarming seeing Epilogue!Discord and Fluttercruel spending quality time together. Their last scene in Dark World Part 8 is particularly touching.
Twilight and Spike's reunion.
Rarity, after having her Heel Realization, is at first in despair, but Twilight immediately hugs her to remind her she's not alone.
Derpy, after 1000 years of just walking and protecting her "muffin", finally is able to stop and have rest with her Dinky safe and sound.
Spike finally admits his new status as Element of Generosity, and gets a big hug from all of the elements.
Twilight confesses to Apple Pie that, as Tragedy, she killed Apple Pie's sister, fully expecting her to hate her. Apple Pie assures Twilight that she understands it wasn't really her, and forgives her for it.
Derpy and Dinky's reunion when the latter is restored by the Elements.
Every scene so far with Twilight and Shining interacting. All involved in the writing have really captured the deep and loving bond these two share.
Especially notable is Shining's sense of pride over hearing about Twilight defeating Nightmare Moon.
Traitor Dash is defeated in the Duel of Tears, but even after having the memory spell used on her is on the verge of sinking into despair, before her friends talk her into not giving up and offering a chance at redemption (and Apple Pie compliments her on her normal colors). They then leave her under the gaze of Minty Pie, who Rainbow vaguely recognizes, who sings her to sleep with the G3 theme song.
There's just something touching about, after a thousand years of self loathing, pain, and being forced to do horrible things, Rainbow Dash finally is able to just rest peacefully, probably having the first good dream she'd had since the Day of Chaos.
At the end of 'The Ultimate Foe', after the defeat of the Valeyard, Rarity finally returning Spike's love for her. Even more touching since 'Secret Of My Excess' didn't happen in this timeline, so this is the first true confirmation she returns his feelings.
Also in 'The Ultimate Foe,' when Twilight is being corrupted by the Valeyard, the mysterious voice, who up until this point has been belittling her and urging her to abandon her friends, suddenly panics and desperately tries to snap Twilight out of it. When Twilight snaps out of it, the voice has this to say:
Its kind of strange, but Discord kind of gets one when, after Fluttercruel is hurt by the Valeyard's sonic attack, he actually goes out of his way to console her, even if he genuinely is incapable of understanding why he's doing it.
Shining Armor 7: Shining had noticed how beautiful Cadence had become after all those years growing up before, but one could probably say that the TRUE romance of Cadence and Shining starts this chapter when Cadence says this:
Cadence: "And that's what I adore about you, Shining. You're one of the few ponies I'm one-hundred-percent sure likes me for who I am. And then you turn around and call yourself an 'acceptable loss!'"
"Love/Hate Bedlam": the fact that Rarity goes into a Tranquil Fury when she finds out what Fluttercruel did to Fluttershy speaks volumes of her close friendship with Fluttershy.
Heck, Rarity managing to shoot down every lie Fluttercruel tried to tell about Fluttershy without batting an eye.
When Spike is feeling that he isn't being helpful to the group, all the others pitch in to reassure him that he is. The voice tries telling Twilight to ditch him and find someone who doesn't angst all the time, she basically tells it to go to hell.
In the "Retcon-Struction Blues" special episode, we see Twist finally accepting that Silver Spoon has changed and accepting her as a friend. It's extremely touching; they both even send a friendship report to Celestia together.
During her conversation with Twist, Silver Spoon lets go of her mother's 'be a lady' orders for a moment and has an absolutely adorable moment of acting like a real child for once. We've seen before she isn't used to actually being able to act like a filly that often, when she does she's really adorable.
Speaking of whom, Celestia and Luna both agreeing that their memories of their family and friends are worth the irreversible separation from the Heart World, even if it risks their world eventually ceasing to exist.
Trixie has really grown up. When Twilight comes to see her, she gives very sound and calming advice to a guilt wracked Twilight on growing and letting go of things. And then they have a sleepover. Awwwwwww.
For some reason, Rarity channeling Flash in Dark World 21 by asking Spike not to kill Angry Pie for Twilight's sake was pretty sweet. Remember, Rarity had just killed Fluttercruel, and she was furious at Angry Pie. However, because of her understanding of truth, recognition of being Not So Different in approach and love for her friends, she disciplines herself enough to try to talk Angry out of fighting them.
In the same chapter, Twilight entering Angry Pie's mind and convincing her personalities to merge, thus managing to redeem her. This is followed by Pinkie talking with all of her friends and meeting Apple Pie properly, and them forgiving her.
In addition, there's How Twilight shows Pinkie the light. She uses a reverse Memory Spell to show Pinkie her memories of Pinkie to show her Discord was lying and she never saw her as a joke, but a friend.
Adding to it? Pinkie makes six. All six of the original mane six are free. Fluttershy may be dead, but she's still in Pony Heaven, free from Discord's grasp. The mane six are saved!
The above sequence also has a couple more for Rarity. First she channels Apple Pie's sister Poison Apple, giving them a chance to say goodbye. Then she channels one of Angry Pie's foals, allowing Pinkie to get some closure.
According to "Shining Armor Part 8", Misfit Actual are such True Companions, Shining would have no problem with any of them dating Twilight. That says something.
Shining helping to pull Ellis out of his Heroic BSOD from the fight with the Hooviets.
"Dark World 22: Off Da Rails" oddly enough has a villainous example. Discord is moping over Angry Pie "dying" (being redeemed), and Fluttercruel comforts him, saying that in the end, she's still there for him, and they only need each other.
Later, there's Discord defyingDevour The Dragon when Fluttercruel begs him to consume her to save himself. Discord's been mortally wounded and denies himself the one way he could save his own life out of love for his daughter, and actually admits he loves her. It's probably the most selfless thing Discord has ever done.
Fluttershy's spirit visiting Rainbow Dash's soul, and convincing her not to give up on getting better. And on top of that, when the subject of Fluttercruel comes up, 'Shy states that she forgives her for what Cruel did to her. Her appearance implies she may have become an angel after dying, it's little surprise.
Fluttershy standing up to the Draconequi and Havoc to rescue her daughter. This is followed by her finally giving Fluttercruel the one thing she'd wanted all her life; a loving relationship with her mother.
Pinkie Pie's goodbye to the group is both this and a Tear Jerker.
When Twilight's entrance exam is brought up, the Interviewers ask Shining whether he was ever afraid of her afterwards. He admits that he was freaked out over the incident itself, but he'd never hate or fear Twilight. The Earth Pony filly interviewer hugs him for this.
Starlight's Nightmare. At the very end of the trial of her soul, she pronounces herself guilty of taking part in the G2 explosion, and the prosecutor in return reveals himself to be The Father Of All Alicorns. He then tells her that in admitting her guilt she had given herself room to be forgiven, forgives her, and gives her a spot in Pony Heaven.
Somehow, the Dark World hero team finds their way to Discord's Art gallery, and discovers the princesses. They free them from their gold statues, and many happy moments happen.
Shady's spirit arriving, defending Discord from the Nameless Passenger's insults, and trying to convince him to redeem himself, showing even after everything he's done, she still loves her son.
"Beating Up Discord" has a brief scene where Pinkie Pie and her foals are seen playing a video game adaptation of her friend's adventure in Pony Heaven. Not only is it sweet to see Pinkie and some of her friends made it to Pony Heaven, she closes it by wishing Twilight and the others luck in whats coming.
In "All Things In Twilight" Twilight sees a memory of Discord sincerely apologizing for everyone he hurt, even though he knows it's not going to change anything for him to do so and its too late to fix things.
The filler episode "Rainbow Dash Prologue" reveals that the reason Rainbow Dash is so loyal to her friends is because of G3 RD's Undying Loyalty to her own friends and desire to never run away from a problem and leave them (like she did during the Cosmic Retcon. Doubly touching, considering the vast majority of the chapter is otherwise Tear Jerker worthy.
Sunset: Circus Girl. Not only did she help save a wedding performance, but apparently she left the family business so her parents wouldn't have to retire. That's some devoted daughter.
Surprisingly, Mortis, alicorn of Death, gets a sweet moment in the dream section of Melody's Gaiden chapter as he talks about why death belongs to the alicorns and existence rather than the nothingness of Entropy.
Celestia gets one when he explains why phoenixes rise from their ashes; she did it to remind mortals that Mortis is the Concept of Rebirth in addition to death as a gift for Mortis, something Mortis is touched by.
Mortis takes part in another in Melody's Nightmare chapter where, after her death, he takes her to his Father, who shows her how music survives the apocalypse through her family, touching her deeply.
The epilogue of Melody's story cuts ahead to present day, to her descendants Rarity and Sweetie Belle. Rarity comforts Sweetie after the seizure caused by her link with Diamond Tiara by singing the song Melody named her daughter after, which she in turned passed along to her own daughter, and down through the family through all the years.
Interviewer's Note (Unicorn): You never thought for a moment she'd done it.
Shining Armor: No. Bucking. Way.
Interviewer's Note (Pegasus): We expected nothing else.
Bright Eye's Gaiden Story has one with her interactions with Wind Whistler and Glory, both of whom befriended her and helped draw her out of her Heroic BSOD.
Bright Eye's not caring about any of the changes the spell is causing; because she knows they'll always be together no matter what.
The Breezies in general are adorable.
Zipzee's refusal to give up hope triggers a miracle, breaking Discord's spell on the Breezies that turned them into Parasprites. Later her refusal to leave Rainbow Dash and Daisyslow refusing to leave her.
Zecora calling Twilight Clover in recognition of the fact they've been friends in all three of their incarnations.
Around this point, the preview pic changes to a hand drawn one of Lancer and Bright Eyes. Why? This little bit from the description:
Night Eyes: Look mom, I drew when you and dad first met.
Bright Eyes being reunited with Glory, Sparkler, and Moki.
The latter especially, as she helps Bright Eyes regain her memories so that she can properly say that she forgives her. Even more so as it was strongly implied that she was going to kill Bright Eyes as revenge for causing the disaster.
Bright Eyes regaining her memories of her and Lancer's relationship and Lancer being so happy Bright Eyes has to give him a "Shut Up" Kiss. Even more heartwarming since it's possible the act that triggered her memories returning also conceived their second child.
Bright Eyes giving birth to Keen Eyes. The fact Glory had managed to get Sweetheart to be the doctor and the strength that gives Bright Eyes adds to the moment.
There's the implication that Pink Velvet had originally intended to take part in a lynch mob against Bright Eyes when the time came...but when it finally does, she can't do it and sends the mob on a Snipe Hunt rather than sell out Bright Eyes.
Bright Eyes' memory of being saved by some coyotes by a deer goddess of some kind and being taught about the compassionate side of nature by her. After the Nightmare Fuel of the previous scene, the counterpoint of seeing lots of mother animals adorably taking care of their children being presented to a little filly was much needed Sweet Dreams Fuel.
Bright Eyes' reunion with Starlight in the afterlife, followed later by being reunited with Lancer upon his death, with them being given their own private afterlife to rollerblade/dance in.
"A Day at the Circus" is this in its entirety... which is exactly the point. Just simply having the Mane Six and their families and friends enjoying the circus and having fun together.
The Loose Canon story "Nightmares' House" shows Nightmare Paradox and her Psycho Rangers having some downtime, and they're all acting sort of like their real selves, especially in terms of how much they all, especially Paradox, care about Nightmare Banneret (Spike) and his struggles with not having Rarity's Nightmare with them and how they all call each other their normal names rather than their Nightmare titles. Word Of God is that he intended it to firmly distinguish his canon's Nightmares as different from the show/comic canon (in which Nightmares are more Demonic Possession than Super-Powered Evil Side) but that doesn't stop it from being touching here and there.
One of the first things Dark World Twilight does as an Alicorn after the Final Battle is to recreate every part of the Super Stallion franchise she can remember for Apple Pie.
Dark World's final chapter is full of well deserved moments: Twilight's reunion with her parents, Rarity/Libra restoring to life everyone who died as a result of Discord's reign who chooses to come back (including Scootaloo, Sparkler, Granny Smith, Magica, Poison Apple, Gilda, and Tom), and of course, Rarity and Spike's wedding.
A small one, but Discord deciding to write a apology letter to Venus for making light of her son's death. This is after experiencing the same thing done to his own daughter ad-infinitum.
Amicitia, as The Voice, convincing Twilight the First to marry Patch and Buddy, and helping her in performing the ceremony. We also see Amicitia comforting a young Discord (the good one) when he has a fever, and visiting Chaos Verse!Discord, who thanks her for giving him hope (as Twilight Tragedy) back in Discord: Not One of A Kind.
Chapter 37 Lighting the Grim Darkness: Amicitia taking on a whole bunch of dark fics and giving them happy — or in some cases, bittersweet — endings.
From Octavia Pie's side chapter, we find out that her special talent is hearing the rhythm of life, and that discord turned that rhythm into a hammering loud noise. However, once Octavia came down to Ponyville after getting Applejack's letter, she found new inspiration in the beat of healing hearts. Making her one of the few side-ponies to be healed BEFORE the Gaia incident.
Shining Armor 16-1 has Shining comforting Cadence after the second fight with Makarov, pointing out that, the fact she's a princess aside, she's his friend and he's there for her.
It also has the Equestrians and Deer Rebels performing a funeral at sea for the Alicorn cyborg Shining Mercy Killed.
16-2 cements Misfit Actual's status as True Companions (as if we needed proof) when Shining Armor tries to give himself over to Makarov to spare the others, only for them all to agree to surrender as well. Shining even says afterwards that they could never be the Elements of Harmony, because they have too many ponies that represent Loyalty.
17-3 only builds on this, as even after being left bloody and beaten by the Hooviets, as soon as the squad is free they don't hesitate to join back up with Shining and help fight back.
A Meta example. After having a falling out that got very heated and a lot of bad blood between them, it seems two of the authors Alexwarlorn and LZ are at least trying to make amends with each other.