Red and Yellow's first encounter, with him getting her a Ratata and telling her no matter what a Pokemon looks like, as long as you are kind to one, they will always be your friend.
Blue was firmly established as a tricky swindler who was out for her own gain. So when she breaks out in true tears of regret for the things she's done combined with tears of joy after being officially granted a Pokedex and a Pallet Town trainer, it's really touching.
After blasting Lance out of the sky, Yellow slips into unconsciousness and into a dream. She wonders where she is and where Pika is. After being shocked at the new forms of her newly evolved Pokemon, she finds Pika and asks him to come to her. Pika runs off and she chases him, confused, until she sees him joyfully leap into Red's arms. She then remembers that despite all the time she and Pika spent together, he is now with his true trainer, and is happy for them. But she asks for just a moment longer for things to be like they way before, and the last image in her dream is her snuggling with her full, unevolved team along with Pika. It was so darm cute.
Pryce reveals that he has been posing as the Mask of Ice to catch Celebi and go back in time to keep a Lapras's parents from dying. After Celebi opens a hole in time, we see the Laprases in question never died and were alive at the bottom of the ravine. The baby Lapras, Glacier, goes through the time hole and then we see it hug it's parents while all of them cry tears of joy.
It's not just that either. Pryce hears the song his friends had made together for him as this happens and his icy heart finally melts; he even starts to cry. He then tells an unconscious Gold to cherish the time he has with his own Pokemon and bids farewell before letting go of the wheelchair he's been holding onto and falling into the time hole. As a Tear Jerker, it's very effective.
Will and Karen essentially Mind Rape Blue, forcing her to have relapses of when she was kidnapped and she's crying in fear. Forcing her to face Ho-oh, the bird that kidnapped her, mocking her the whole time. She nearly faints and then takes solace in the fact that she got Silver to a safe place, only to have Will laugh at her, reveal that Silver got there before her and they've already beat him to the point that he can no longer move. She crawls over to him, confused, thinking she had gotten him somewhere safe. Here's where the heartwarming happens, he explains how he got there and when she asks why he came back and put himself in danger, he says it was because he wanted to fight alongside and protect her before passing out. Blue has memories of her time with Silver going through her head, meeting him, taking care of him, naming him, making gloves for him and escaping with him. Will and Karen keep mocking her, but now Blue's PISSED. Ho-oh flies by her again, but this time she's completely unfazed, she then gives a Badass Boast about how she's overcome all of her fears and weaknesses. When Ho-oh comes down again, she unleashes the legendary bird trio and gets to have her Mama Bear moment in the ensuing battle. All of which shows that the love she feels for Silver outweighs the fear she had of birds and was what she used to overcome that fear, and that Blue and Silver love each other more than they hate their past.
This Troper saw Mimi's return to Ruby in RS as a Crowning Moment of Heartwarming, especially when the latter finally learns the meaning of inner beauty and acknowledges Mimi as coequal to his other team members.
The reason why Deoxys targeted Red: Deoxys had absorbed Red's DNA when he had escaped from a lab and had assumed he was his ancestor - his only family. Unfortunately, the only language Deoxys knew was fighting, so it wasn't till Red defeated him that all of this was found out. What brings the warm fuzzies is this revelation and when Red accepts him as one of his "pals."
Also, when we find out that Giovanni was actually Silver's father. Both of them were falling from a ship and into a burning wreckage. To protect the unconscious Silver, Giovanni lifted up his son with one arm to protect him from the flames. He mused how though his body is getting weaker from a disease, he is glad that he was able see his son one more time, saying how much Silver has grown.
Then, when when Silver wakes up, he realizes that Giovanni is his father, much to his horror and disgust. Blue (Green in Japan) however angrily points out that Giovanni shielded him from the fire, willingly allowing himself to be burned to save his son, and searched long and hard for ten years to find him.
Green: "There is no reason why you shouldn't be proud of a father like that."
And Silver breaks down, falling to his knees, crying over Giovanni's unconscious form, calling him "father".
Oh god the 'Vs. Pachirisu' chapter of the DP arc. After the other competitors go out of their way to sabotage Platinum's attempts at her first contest, she loses composure and decides to forfeit despite how hard all three Dex Holders worked to prepare for it. Then Diamond gives her a slice of pie he made himself and gives a little speech about how scary performing for others can be but how he loves doing things happily and how good food helps. Regaining her confidence, she dominates the contest with a smile, and when presented with the ribbon, she drags Dia and Pearl up with her on stage, saying that all three of them won together and that she should've done this before when she won her badges.
Of course, what helps is that there's a different kind of crowning moment sandwiched in there. Fantina, who was attending the contest and has taken a shine to Platina's performance, managed to root out the snobby saboteurs who messed with Platinum during the contest and commanded her Drifblim to treat them as they rightly deserved - by hauling them out to the trash bin! This is one of those rare heartwarmers with a side helping of karma for good measure.
After telling them off for lying to her about their identities, Lady Berlitz's apology to Dia and Pearl for every single time she lied to them during their journey. Something that had been always played for laughs.
A equally tear-jerking and heartwarming example, where when Pearl, Diamond and Platinum split up to the different lakes, they all reminiscence about how they start their mornings everyday, always with the Pokedex beeping due to the Resonance System, to let them know they're all together. When it stops beeping when they split up, they all cried, realizing how much they depended and missed each other, even if they were only separated for the moment.
In order to be able to save Uxie, Mesprit, and Azelf from confinement, the DP trio must push a corresponding button for each machine that frees them. The problem? They are being blocked by enemy Pokemon. So what do they do? They give up their Pokedexes (which the enemy is interested in) to buy time to push the buttons while the enemy grabs them. The heartrending part is that even though the symbol of the trio's friendship is now gone, it doesn't in any way lessen their bond.
Dia's entire speech about his concept of what "space" and "time" means to him. Also counts as a CMoA for the events that happen afterward because of it.
Wake was revealed to have recorded a song for his student, Pearl. The fact that Pearl was about to cry only make it even more touching.
Platinum cheering Palmer up about how Pearl had always looked up to him and become very strong even though he's rarely by his side. It's sort of touching how Palmer thinks of himself as a "pathetic father" for not being there when his son was in a dangerous life and death battle, and yet, he actually did well enough to raise him in battling. So, the fact Pearl survived to this very day is actually thanks to him even though he believes he hasn't done enough to be by his side.
The reunion between the bodyguards and the Sinnoh trio. Tears and hugs abound, and it even turns out that Dia and Pearl saved Paka and Uji's sunglasses and kept them with them the whole time.
Cyrus' Heel-Face Turn and parting words to the Sinnoh trio, and his three young commanders (Saturn, Mars and Jupiter) staying with him out of Undying Loyalty despite him disbanding Team Galactic.
The contents of Professor Oak's letter as well as Shaymin leaping into Cyrus's arms with its flowers blooming.
The ending. Especially when Platinum asks Diamond and Pearl to perform one of their double-acts for her before battling Palmer, and the genuine smile she gives when we see her as their sole audience member.
Silver says that Crystal shouldn't need to help him out in the fight against Team Rocket, but Crystal says that she doesn't want the kids at the Academy living in a world where bad people are free to roam around. Not to mention how she pulls out her Pokedex and reminds him that they are friends.
Giovanni shows up at the Sinjoh Ruins along with Silver's Ursaring, which promptly proceeds to kick Petrel's ass. When Petrel weakly manages to joke about how strong Ursaring is, Giovanni's response is basically, "Duh, my son raised it."
Also, Giovanni remains the evil leader of Team Rocket...but when Silver swears he'll oppose him, he insists that Silver train with Lance and Pryce to become strong enough for that. To hammer the point home, he thinks in his head that if he is to fall to anyone, he wants it to be his son. Even Evil Has Loved Ones indeed!
There's something oddly sweet about Black cheering up Hiker Andy after the older man admitted to him how he had nearly given up his dream to compete in the Pokemon League due to his fear of fire. Bonus points Black pointing out that Andy's Cottonee was trying to help its Trainer by forcing itself to go near flames despite being weak to them. Hey, old people can still have dreams To Be a Master too.
By the time the story arrives at Nimbasa, Black clearly shows that he has grown to care greatly about White and is now fiercely protective of her, as demonstrated when he spends the entire night searching for her when she goes missing, and immediately sends out his Pokemon in rage when he thinks he found the one responsible. He's come a long way from being the self-centered prick from the beginning who blew off his own friends to chase after his own dreams.
The train scene, dear Arceus. To elaborate, Black has refused to go on the Battle Subway, out of consideration for White. But White accepts the challenge, in order to improve her trainer skills for Gigi to have other options to return to. At first, Black is jealous of White, since she get's the opportunity he's missed out on. However, after some thougth, he makes a major effort to aid White, and helps her catch a Deerling for her team. When its finally time for White to leave on the subway, he says goodbye to White, reminiscing about the small amount of time they've spent together while traveling. He then asks White how much debt he has left, and when he is told he has a little bit left, Black promises that, once he's beaten the Pokemon league and accomplished his own dreams, he'll return and work off the remaining debt, just like White asked him to. He also throws War to her, giving her the third Pokemon she needs to be allowed to compete in the challenges. Quite a change from the Black who was utterly focused on completing his own dreams and leaving his friends behind in order to do so.