It's established that many of the oldest loopers (Ranma and Naruto for sure, probably more) are so powerful that they are just a single step away from ascending to some level of godhood. Yet none of them have. Why? Because doing so would destroy their home universes, and despite everything, they still care enough to not want that to happen.
Special mentions goes to the newly Looping Dumbledore and Harry putting their differences behind them, even if it was from the Spacebattles Loops. Innortal was a blatant Dumbledore basher, and the scars from that passed on to the Spacebattles loops regardless of what opinions anybody there held about him. When he began Looping, Dumbledore even suffered from every flaw that was presented in him back by Innortal, but then he met Thomas Light. After seeing somebody act like he felt he should have in the baseline, Dumbledore went off to correct his mistakes immediately, and has become one of the most common Looping Harry Potter characters to have something written about him.
The MLP Loops:
After Twilight goes through a Past Sins variant loop, she is devastated when she realizes that her adopted daughter is lost to her. Fortunately, Nyx is treated as an alter-ego of Nightmare Moon and can sidestep the "no children" rule. Appearing near the default loop start point, the two are quickly reunited.
Discord strands Applebloom and Diamond Tiara on a small island. They put aside their differences to concentrate on survival and discover they can actually get along pretty well. This is reinforced in a later loop when DT lets AB know she's now Awake.
Twilight puts Nightmare Moon through therapy in one loop, eventually getting to the root of her villainy and making her break down. This purges her of the corruption and returns her to being Luna. Then, the rest of the Mane Six (and Spike) walk in after spying on the session, and tell Luna that they all forgive her for trying to plunge the planet into eternal night.
The moments between Spike and Rarity, leading up to the two getting married.
The whole getting married thing is even better, because it's the first, and currently only, marriage that exists across loops. Hundreds of loopers show up to attend, and the few who don't send their fondest regards. The loop ends just as their honeymoon starts, but the Admins decide to give them a loop to enjoy together as a married couple.
Smaug rejecting part of Sombra's treasury because the memories of the loop are treasure enough for him.
Three Words: Ganondorf, Pony manestylist. Because the Gerudo prided themselves on horsemanship, and Ganondorf loved taking care of his warcharger, he decided to take a break from his usual routine and be a mane stylist. He does quite some excellent work. Including braiding ethereal manes.
A offscreen one, but the Slavequestria version of Pinkie Pie was running the underground railroad to help escaped slaves escape to the Griffon lands.
In chapter 80, Derpy's cutie mark talent was explored. Some explorations were Awesome (Derpy's ability is entropy, Derpy can walk on water bubbles, she can read minds via "thought bubbles"), some were funny (It is just her basic personality, She is a collective of multiple faulty Mirror Pool clones, she is the child of a Mirror Pool clone, she can create atmospheric mirages and uses them to get out of taking care of Dinky.) but some were heartwarming (She can make animated bubbles and throw her own voice to create bubble puppet theater plays for Dinky, She can see alternate realities and Dinky is a last survivor replica of her that she rescued from an Equestria that was destroyed by Smooze.)
In one loop, Twilight Sparkle loops back far enough that she manages to befriend Sunset Shimmer, and tells her that she's looking forward to the next time together. When Sunset finally starts looping, after many fused loops, she goes back to Equestria, revealing herself with "I have been, and always shall be, your friend."
The first time the Mane Six looped into the Hub Loop (i.e., our own real world), and had a chance to speak to the authors of the fictional work in which they appear here. Now, when this happened to the Naruto cast they did a full-on Rage Against the Author (see the entry on the main page for details). What do Twilight and her friends do? They write a letter to the show-runners:
Excerpt the letter: ... by a cosmic coincidence it would take too long to explain, we have ended up here on your Earth. We only have a relatively short time here before we must depart anew, but we feel that we owe it to you, if none other, to tell you how grateful we are. In a way we cannot understand, you may have created us. If that is not the case, then you faithfully recreated us and told our story to millions. So thank you. Yours sincerely, Twilight Sparkle, Pinkie Pie, Rainbow Dash, Fluttershy, Rarity and Applejack. P.S. please find enclosed some photographs. We're sure you'll like them.
And then they went to an MLP fan convention and pretended to be cosplayers.
In Loop 78.5, Twilight decides to let Nyx share her last name, even in loops where ponies don't use surnames. Nyx is, understandably, moved to tears by this.
The fact that as soon as they discover what's causing the Infinite Loops and that its a multiverse-wide phenomenon, the ponies dedicate themselves to making Equestria a "Sanctuary Loop" where any looper visiting it will be given all the emotional support the ponies can provide so long as the looper is actually trying to coexist semi-peacefully. Since the greatest danger an Anchor faces is going insane from the sheer endless repetition of the Loops (see the Go Mad from the Revelation entry in the main Loops page for more details), this ultimately leads to saving the sanity of several Loopers and at least one Anchor — and the worst-case scenario for an Anchor going bugfuck is the loss of their entire Loop. So Equestria has actually saved entire chunks of the multiverse from oblivion, by the Power of Friendship.
Sleipnir (Yggdrasil Sysadmin for Equestria): The fact that you have all, of your own volition, offered sanctuary to other loopers who visit Equestria is more than we could have ever asked for you. That you manage to succeed despite the numerous significantly dangerous hostile entities native to your Loop is nothing short of a miracle. You've already managed to avert at least one potential metaphysical collapse of another Anchor, likely saving Miss Clearwater's entire Loop in the process. You have already gone above and beyond the duty assigned to you as Loopers, and I hope you will continue to do so. I am honoured beyond words to be your assigned Administrator.
In addition to preventing the complete metaphysical oblivion of the Twilight loop, the ponies' outreach efforts have resulted in at least two universes formerly stuck as Read Only for lack of viable (or sane) Anchor candidates to become fully functional loops, due to Fluttershy's befriending of Leman Russ (making him able to handle being the Anchor for the Warhammer loop) and Twilight's redemption of Skynet (making it eligible to become the Anchor for the Terminator loop). Greater love hath no pony, indeed.
Twilight's "heartsong" when she decides to start out a 'vanilla' loop by actually accepting that party invitation instead of staying in her tower and reading the legend about the Mare in the Moon. Sure, its actually Looping Twilight and she's already learned this lesson thousands of years ago, but her going out of the way like this to let her fellow unicorns in Canterlot know that she really appreciated the effort is still a CMOH. And the author setting the tune to the lyrics of "The Success Song" definitely didn't hurt either. Makes you wish this had happened in the show!
My researches they were enough And keeping my work up to snuff Ponies as friends I did not miss But I wasn't prepared for this... Who'd have thought that chatting was such fun Learning about ponies one by one Sharing mem'ries and helping them out It's a wonderful new feeling without doubt! Companionship that I did dismiss Now I know that it's simply bliss Making some new friends Helping ponies Seeing what life sends Not books only I want to do more of this!
In Loop 62.6, Twilight and Silver Spoon became the voice actors of their equivilents for the show. The funny part was, Twilight didn't think that she was like Raven at all. The Heartwarming moment was Silver playing as Shannon Chan-Kent: when she sang the main theme, she teared up about it, because it is a lullaby in Equestria.
Celestia reveals to Big Mac that her favorite thing about the loops is that now she can make friends without the fear of outliving them.
in a later loop, Discord tells Tirek something similar, though the context is different (not revealing the existence of the loops).
The Yu-Gi-Oh! Loops:
Fire Emblem Awakening Loops:
Robin's Determinator status. Not even the Gods turning him into a girl could stop him from being with Lucina and Morgan .
Loop 1.7 has Robin and Luncina in the Hub loop, simply relaxing and living like normal people. Considering the hell they go through in the baseline, this troper though they deserved it.
The Mega Man Loops:
Doubling as a Tear Jerker, the vigil for the Lost Loop (the loop that was annihilated in the process of bringing the Mega Man loop baseline online). The author's note just adds to it.
The Story of Simon's loops and his encounter with the world of Uzumaki.
Johnny Joestar being stuck in the loop and saying the one good thing about his situation is being with Gyro Zeppeli, his best friend, once again. He died at the end of Steel Ball Run.
Raditz from Dragon Ball getting a loop where he is a hero and beloved by the citizens of Wall Maria after years of being poorly treated by fans, and by a loop writer who had previously made a Raditz is weak joke at that. Pity he won't remember it due to him not being a looper, but Goku, Armin, Mikasa and Eren will.
In a "Sailor Moon" loop based on Shadow Jack's "Where I Watch Sailor Moon" thread, Usagi gives the Holy Grail to Hotaru a.k.a Sailor Saturn.
An incident in HTTYD loop 6.2, where Hiccup and Toothless go Skrill-catching. This involves Hiccup jumping off Toothless' back at the Skrill in the middle of a thunderstorm, tagging it with an item, and falling off – only to be caught again by Toothless. This is all planned out, and is a beautiful expression of trust.
A majorly painfull incident involving Awake!Link forging a super sword and trying it out in a baseline loop, Awake!Navi feeling worthless thus having her forge her own sword and gain sword skills so she can show Link that she is not worthless, and thus the fight with Dark!Link being majorly brutal with a trip to Eiken being the end result. After they get back, Navi vents her frustrations at Link about being worthless. Link confesses that he knew that Navi has a life beyond being his partner, and swears to be a better partner and friend to her.