A meta example, but during the launch party of Final Fantasy XIV: A Realm Reborn in Japan, director Naoki Yoshida shed Manly Tears after years of hard work revamping the game from the ground up while receiving a great amount of support from fans.
Raubahn's Undying Loyalty to the sultana, especially when he props the little lalafell queen up on his arm.
Everyone remembering you're a Warrior of Light in the ending cutscenes, if you're a Legacy veteran.
F'lhaminn reuniting with her adopted daughter, Minfilia, after being away from her for so many years while watching over her from a distance as her daughter grew up to be a successful and strong woman.
During The Three Collectors arc of the Hildebrand quests, we're shown that while yes, Hildebrand is an idiotic bumbling fool, his desire to help people with their problems is true, as he happily helps a the neglected daughter of an Ul'dahn noble woman with recovering a vase she had dropped while bringing home to avoid a monster attack. He helps get the vase repaired and restored by his father, Godbert despite his misgivings and disagreements with him over inheriting the family business, preferring to be an inspector. Despite failing to stop the thief from stealing a treasured sword, he helps the before mentioned mother and daughter connect via a good laugh caused by his antics.
The cutscene for "The Rising" anniversary event is definitely this, as another "meta" sort of example. The dev team, led by Yoshida and in the form of the Wandering Minstrel, takes the time to thank you, the player, for sticking with XIV through thick and thin. That they went through all that trouble, just to thank you, says volumes about how grateful they are everyone gave them a second chance.
The end of "The Beast Within" quest. After being stuck as a Tonberry and stirring in rancor for 1500 years, the Scholar who your fairy, Lily, originally belonged to could tell one another apart despite the changes. He warned her to stay away despite the rancor and tried to keep her safe by running inside so he didn't hurt her, and she stopped him from being killed and cured him of the hatred that left him tormented.
A player by the name of Codex Vahlda, who enjoyed playing the game as a level 50 Bard, had passed away from renal failure. When news of his death caught on, hundreds of players from several servers held vigils within the game to honor the passing of their fellow player. The gesture from so many players, including those who did not know Codex personally, is both heartwarming and tear jerker worthy.
Heavensturn 2014 has two warming entries:
In Aleport, a mother is worried sick over her baby because it won't stop crying. At first, she believes that her husband's ugly face caused the baby to cry. When your sheep companion uses its soothing sleep magic on the mother, she realizes that it was her own worry and fears that was causing the baby to cry and after being calmed down herself, the baby also calmed down.
Bentbranch Meadows has a travelling merchant who is worried for her chocobo since it refuses to eat and has become very restless. You discover a chocobo tail feather nearby and showing it to the chocobo calmed it down a little bit. After having your sheep put the chocobo to sleep, showing the feather to the chocobo handler reveals that the feather belonged to a chocobo that was a mate to the merchant's chocobo. Said mate was bought by someone and they had quickly left before the two chocobos could reunite, which caused the merchant's chocobo to become heartbroken. After sharing the news with the merchant, she decides to sacrifice her profits for the day so that she can help her chocobo find her lost mate. Aww...
When you being the quest to explore Wander's Palace again (hard mode), you run into a couple who ask you to save the Tonberries inside. Why? Because after they were stabbed by one and left to die, the defeat of the Tonberry King lifted the curse on the Tonberries, making them calm and nursed the wounded couple back to health. As you explore the Mamool Ja infested palace, every Tonberry you save thanks you for rescuing them.
The couple themselves is this for members of the LGBT community. The two are a gay male couple that were kicked out of their home village...because one of them is a Miqo'te and the other Hyur. The fact that they're both male isn't even brought up and the two specifically point out that despite being entirely different species their love is the same as anyone elses.
And for those who have completed the Scholar quest chain, you find out that Surito (the tonberry scholar you helped out) is alive and well, and making good on his promise to help his fellow tonberries. In fact, he even appears in the dungeon, right past the first boss.
In addition, for those playing a Scholar in the dungeon, the mere fact that you are bringing Lily (in either Eos or Selene form) back home to save her people is kind of heartwarming in and of itself.
The end of the 2.55 story line is full of this towards the player. You're accused of killing Nanamo and are branded as a traitor by the Monteraists and the Crystal Braves. Raubahn, before he attacks the true culprit, tells you that not once had he ever doubted you. After escaping by yourself while the Scions stay behind to hold off the corrupt soldiers, you can talk to several NPCs in each city and learn that they're still on your side; the commanders in each Grand Company believe you are truly innocent and refuse to believe that you, a Warrior of Light, would murder someone. If you completed a level 50 crafting/gathering class and/or a level 30 disciple of war/magic, the guild masters in their respective guilds tell you that you have their full support. For a major Wham Episode where it seemed everyone you know has betrayed you, it's heart warming to see everyday people who still believe in you to the very end.
Not just guild leader, but plenty of others, your initial escape, is facilitated by a simple chocobo carriage (the same one that brought non-Legacy adventurers to their starting cities). The owners of all three cities adventurer pubs flat out say they trust you, as do those with close contact of the city leaders, with Gridania and Limsa informing that they've informed all in the know that you are to be granted free movement through their cities, and declare you innocent. The knights of Ishgard, who probably not happy at some the accusations pointed their way by the conspirators, likewise intend to repay the Monetarist Hospitality with their own, with the leader of House Fortemps even declaring that any attempt to enter or cause trouble within Dragonhead, or the surrounding area in search of you and the Scions will be denied entrance. Knowing so many people are completely on your side will brighten your mood, given the dark ending of the 2.0 story.
Speaking to Haurchefant following the story's conclusion and the credit roll will have him truly prove how loyal an ally he is to you reassuring you that the horrible chain of events that took place in Before the Fall is not the end for you, guarantees your comfort and safety, and vows to stand at the side when the time comes to redeem yourself and take revenge against the monetarists.
Haurchefant: Do not hesitate to call upon me, regardless of hour. My home is your home, and I would see you afforded all comforts and courtesies. Rest and regain your strength, <name>. You shall have your redemption and your reckoning in due time—and when that day comes, I shall stand at your side.
Also from patch 2.55, is a "Level 22 Postmoogle" quest, involving Wymond, a minor NPC who's an Information broker, that the player deals with from time to time is mistakenly given a ransom note meant to be given to a Raymond due to the illegible name written on the envelope. He reveals during the quest, that he chose to hang around that spot of town, as that's where a flower girl named Myrtha, before the Calamity hit, used to stand there, and he'd always buy a flower from her to remind him there's good people in the world. He also reveals, that he used to part of the gang that has now taken Raymond's daughter, but left it, after the gang killed Myrthas brother, causing him to make a Heel–Face Turn when Myrtha vanished as well. He revealed the culprits to a certain Gentleman Detective who did solve the case and had them all of the gang locked up. After setting up an elaborate scam to draw both his former gang, and the corrupt merchant who hired them to kidnap Raymond's daughter to steal his land from him via ransom, rescue the girl and take care of the criminals for good, Raymond's wife, gives a flower, and a note as a token of thanks to Wymond. They both reveal she's Myrtha, making Wymond happy to know she's doing alright after all these years, and now happily married with a good family. And, he plans to use the left over money he generated from the plan to rescue Myrtha's daughter to help out the orphans of Ul'Dah.
The 2015 Rising Event follows up the previous event of the same name and cranks it Up to Eleven, You're whisked away to the 18th Floor, which dives heavy into Breaking the Fourth Wall by introducing you Yoshida (the game's director) and the rest of the developers of the game. The entire team thanks you, the player, personally for sticking by the game for over 2 years and hope you keep playing and enjoying the team's work for years to come. Yoshida then goes on to say how Final Fantasy XIV was a failure during 1.0 due to the development team getting too arrogant and that they must never forget the failures of their past in order to continue to make the game of today better and better with each passing moment. Between being thanked personally by the development team and seeing that they do not want to repeat the same mistakes they made from 1.0, it's hard to not crack a smile or shed a few tears.
One of the side quests in the Dravanian Forelands has you helping out a young dragonling with various tasks, such as gathering food for himself and his mother. During each quest, the dragonling takes an interest in you since it's the first time he has seen man with his own eyes and is intrigued by the good deeds you have done for him and his kind so far. Later on, you meet the dragonling's older brother, who immediately casts doubt on you because of man's past sins and forbids his younger brother from interacting with you. The young dragonling is now heartbroken and confused because he knows his brother isn't lying, yet you are not what his brother says. You reassure him that you are who you are and he thanks you for putting his fears at ease. In the final quest in the chain, the dragonling's brother is sick and you're tasked with recreating an ancient medicine that would heal dragons. Once you give the medicine to the dragon who doubted you previously, he still acts suspicious of you, but he says he won't forget your kindness while the dragonling promises to tell his future generation about your good deeds.
In a similar vein, one of the Vath quests has you looking for a dragon mother's son who had been out all day playing. When you do find the young dragon pup, he runs away from you several times because he likes playing games where people chase him. When you finally corner him, the dragon pup thanks you for playing with him and how you were faster than the Vath who chased him. After you report back to the mother dragon, she says how her son came back home and promptly fell asleep with a smile and she thanks you for playing with him since her son rarely ever gets to play with people that are not dragons.
The Level 52 Bard Job Quest has the ever dutiful Sanson telling you that the very self-driven bard Guydelot has gone chasing after an Ishgardian Knight after the man's lover claimed he was a superior singer. Not only was Guydelot following leads for the overarching quest you're on together, but he followed the man's patrol out into the wilderness of Falcon's Nest. Why? To deliver a birthday gift from his love, which carries a message that informs him that she's pregnant with their child! After saving the lives of him and his patrol, he is so overcome with joy that he pledges full support to your group's quest.
"'Tis time to wake up, your Grace. Another day begins in Thanalan, and the sun blazes bright upon the sands." Just the look on the big guy's face, like he can't decide whether to smile or burst into tears.
After the events of 2.55, Alphinaud has made the tough decision of disbanding the Crystal Braves. only to find out that before he could even say the words the remaining loyal members have decided that they were going to stick together regardless because they believed in him and his ideals so strongly, to which Alphinaud can only respond with teary-eyed gratitude.
Making this more heartwarming is that one of the aforementioned loyal members is Alianne, the person you were supposed to meet before said events in 2.55 happened. It was speculated that she was either on the run, captured, or worse in on the coup, or even worse killed like Wilred was. To know that a character you've known even before joining the Scions is not only okay, but still among the good guys is heartwarming in itself.
Despite all of the hardships they encounter during the Astrologian Job Quest, Jannequinard keeps inspiring Leveva onwards because it gave him a purpose in life when no one expected him to. And her father was his Only Friend, so he wants to see to it that his dream lives on despite the risk to himself.
Sidurgu and Rielle's interactions with one another. Despite everyone seemingly wanting to kill her, he stands guard over her and looks after her.
The 2015 Starlight Celebration has the Adventurers' Guild trying to revive a long forgotten part of the story regarding how the celebration came to be. Namely, that when the Ishgardian knights set out from their barracks to find and bring orphans back to their barracks for shelter from the winter weather, they would play a certain melody on their signal bells to let all know they were now seeking to help those in need. The hope being, that by bringing this part of the story back into the celebration, the bells would add an extra amount of festive cheer to the faces of the children of the realm. Cue a team up between Ishgard (who sent the original signal bells that would've been used, which were held in storage for untold years), the player getting repair materials, a famed Eorzean composer to complete the full melody, the "Saint of Nymeia"/Godbert Manderville finishing the restoration and improvement of the bells to increase it's tone and note ranges, and his Little Helpers note (Julyan Manderville, and ALL of the Disciple of the Hand class guildmasters to help decorate, and the Adventurers' Guild sharing the news of the celebration to children all over the realm so they can hear the bells ring again.
When players learned Yugiri's then-current English voice actress was found murdered in her own home, many players honored her memory by going adventureing with the Wind Up Yugiri minon at their side.