The first episode, for starters. After having spent the entire episode mocking and shocking Ash, Pikachu saves him from a flock of Spearow in the middle of a thunderstorm. In the morning after, an exhausted Pikachu still gives Ash an affectionate lick on the cheek, cementing the start of an everlasting friendship.
Pikachu's Goodbye: Upon discovering a Pikachu colony in the woods, Ash tried to abandon Pikachu, thinking it'd be happier living among its own species. But Pikachu decided to stay with Ash in the end.
Ash: Pikachu was my very first Pokémon...
The end of Holy Matrimony is also a sweet moment for Jessie and James, as well as one of the first major Rocketshipping hints fans discovered. The fact that they accidentally leave poor Meowth behind isn't as heartwarming, although his reaction is cute.
James: "Double trouble time, right?"
Jessie: "Sounds great to me, James."
It's heartwarming if you're a Rocketshipper. They were so busy staring into each other's eyes that they completely lost focus on what they were doing... and then Meowth yells, "You forgot Meowth again!", implying that this has happened before. (For the record: non-shippy hearts are also nicely heated by this. Friends or lovers, those two are closer than anyone.)
In Snow Way Out, Ash gets trapped in a cave during the blizzard and tries to convince his Pokémon to stay warm in their Poké Balls. But they refuse, instead snuggling up to him to keep him warm.
Ash"(getting all teary-eyed) "You win. I guess we will be cold... all together. That's right... all together."
Think about this for a second. Ash Ketchum is wearing nothing but a T-shirt and jeans (he took off his jacket to keep his Pokémon warm in their Poké Balls), blocks an opening in the snow wall they made with his body, and still tells Pikachu to go into his Poké Ball, knowing that Pikachu would be warmer in there then out in the cold with him? If you didn't cry, you have no soul.
In "The Tower of Terror" after Ash and Pikachu had been knocked out by a chandelier, separated from their bodies by Haunter and spent a little time getting to know the three Ghost Pokémon a little better, Ash tells the Ghost Pokémon that he can't stay with them because he needs to continue his journey. Ash, Pikachu and the three Ghost Pokémon return to where Ash and Pikachu's bodies are, and discover that Misty and Brock have pulled them out from underneath the chandelier and are trying to wake them up. Seeing how worried they are, Ash and Pikachu quickly return to their bodies and wake up. Brock and (especially) Misty are relieved to see that Ash and Pikachu are alive. It's a pretty sweet moment.
Seeing Sabrina going through the Defrosting the Ice Queen process in the episode immediately after that, and being reunited with her family thanks to Haunter making her smile for the very first time in her life.
From the first season, Princess vs Princess. Jessie loses the contest and thus, the only chance to finally win a Princess Pokemon Doll Set (it was the first year she would be able to actually enjoy the Princess Festival). To make up for it, James, Meowth and the other Pokemon dress up as the dolls and make their own doll set to cheer her up. Not to mention how the episode is one of the few where Team Rocket doesn't try to steal Pikachu or any Pokemon, showing that they're more than just criminals.
The never-aired-in-the-US episode The Legend of Dratini from Season 1 has one, when the cold, bitter, trigger-happy Warden reunites with the Dratini he left hidden in the Safari Zone 30 years ago. Seeing that it's evolved and has a child of its own invokes the feeling of reuniting with a friend (or perhaps even your own child) who you haven't seen in so many years and knowing that they've lived a content and happy life; it's enough to bring the tears running, as both Kaiser (the Warden) and the (now-)Dragonair cry as they embrace for the first time in decades.
The Problem With Paras, especially when Paras evolves into Parasect. This is quite possibly one of Meowth's sweetest episodes.
At the end of Make Room For Gloom is a rare instance of a heartwarming moment between two characters who only appeared in one episode. Florinda Showers, who now feels confident enough to run her family's nursery because of how well she learned to train her Gloom, proposes to fellow employee Potter to help her run the nursery. The way she tells him "I love you!" is sure to get you every time, followed by him openly admitting his feelings back.
Potter: "I've loved you since the day I saw you, but I was too afraid to tell you!"
What makes this even more heartwarming is that it's also one of those rare instances where some true romantic relationships are involved, even between two one-time characters.
Anytime Misty interacts with the youngest sibling in a family, like Mikey, Sakura, and Max and even acting like as an big sister mentor to them. It helps that Misty herself is the youngest of her own sisters, being able to sympathize with them.
Likewise, any interaction she has with Pikachu is just as sweet, such as when Misty asks to borrow the boys' Pokemon for the Princess Festival tournament battle. Pikachu immediately jumps out of Ash's arms and agrees to battle for Misty.
Island of the Giant Pokemon has a couple of moments between the Pokemon themselves:
First off we have Ekans and Koffing refusing to attack Ash's Pokemon because there's no such thing as a bad Pokemon. In return, Pikachu lets the two of them eat with the group instead of tying them up.
We then have a second heartwarming moment later on at the "Oden" stand, where Ekans and Koffing are crying. What's Pikachu doing? Comforting Ekans by patting it on the shoulder and giving it a look that says "Cheer up, it's OK."
Bound for Trouble: Pikachu and Meowth spent a good chunk arguing (the former usually winning via Thundershock), but then they come upon an apple tree. Pikachu gets there first and takes the fruit, once again smacking Meowth around to get it...and then shares it. That, coupled with Pikachu falling asleep in Meowth's lap, is without a doubt the most "awwww"-inducing scene of the entire Orange Islands arc.
More Team Rocket Heartwarming: in one episode, Meowth runs into a Cargo Cult who begin worshiping him because they mistake him for the "Great Meowth of Bounty", who can use Pay Day. However, those who remember the Scratch Cat's backstory know that Meowth hasn't learned Pay Day yet, nor will he ever (he utilized his intelligence to learn human speech, so he's unable to learn Pay Day). When Meowth is led into an arena, he tries to use Pay Day, but fails. Then, a few seconds later, money starts flying into the arena. It turns out that Jessie and James were throwing the money.
The previous instance gets even more heartwarming when James, having run out of money, throws his favorite bottle caps instead.
It's one of the few instances of the "friendship is more important than money" Aesop that actually works.
Meowth also gives a wonderful little speech at the end of the episode (after which Jessie and James even recite a special version of their motto for him):
Meowth: "You think I'm supposed to be this great cat... but I'm just a big rat. There's only two people in the whole world who ever really cared about me. We messed up a lot, and we used to fight with each other a lot too, but... no matter how bad things got, we always had each other. I thought I was happy here without 'em, but now I know that having them was my real happiness!"
In The Stun Spore Detour, Ash, Tracey and Jessie all get sprayed with a Vileplume's Stun Spore, forcing Misty, James and Meowth to search for some Salveyo weeds to cure them. Misty finds them first, and foils multiple attempts by James and Meowth to trap her and take it for themselves. But when she finds out that Jessie is sick as well, Misty leaves some for them. James and Meowth repay the favour by keeping Jessie from attacking Ash in his weakened state.
Expanding on this, when Jessie finally recovers and discovers that Ash has ALSO recovered, she proceeds to launch a one-woman attack on them. What are James and Meowth doing? Hiding behind a rock and outright refusing to help her because doing so would mean attacking the girl they helped!
Charizard Chills: Charizard ends up getting humiliated and frozen by a Poliwrath and is hit with a case of Break the Haughty, Ash spends the whole night trying to warm up Charizard to defrost him and tells Charizard that whilst he knows that he makes a lot of mistakes and isn't the best trainer, he hopes that someday he and Charizard can battle as a team. Charizard remembers that Ash saved him as a Charmander and despite how disobedient he's been since he evolved to Charmeleon and then Charizard, Ash still hasn't given up on him and never will. Ash finally earns Charizard's Undying Loyalty for the rest of the show.
Ignorance Is Blissey. Seeing Jessie trying to do so much for her friend from Pokemon nurse school. The flashback crosses over into Tear Jerker territory, too.
And James and Meowth instantly stand by her to help protect Blissey. Team Rocket set themselves up as the villains and put on an even hammier performance than usual while not putting up a fight at all.
James:(through a megaphone) "Oh look, Jessie, we dropped all the food we stole from the Pokémon Center."
As sad as it was, the end of "Charizard's Burning Ambition" has Charizard roaring "goodbye and thank you" to Ash. Charizard and Pikachu also share a nice goodbye. It seems like Charizard promises to raise the bar for his species.
All of Lapras of Luxury. Just imagine if Ash's other released Pokémon returned to him like that.
From the Johto episode Hour of the Houndour. After Ash rescues a pack of wild Houndour from Team Rocket, he cheers "We did it!" happily. The four Houndour that were caught then run over, tackle Ash to the ground, and start to lick his face happily. Ash giggles, yelling "Cut it out! That tickles!" It's a little thing, but it shows how wild Pokémon aren't really wild, and will show gratitude to anyone that's willing to help them no matter what.
Another Johto episode, Great Bowls of Fire. The scene before the theme song showed that Ash's Charizard had come along with Liza to Blackthorn City. After Charizard greets its trainer with a Flamethrower to the face, it flies into him, knocking him over. The next shot is of Charizard licking Ash's face while Ash laughs and says "It's good to see you too, Charizard! You haven't changed a bit!" showing that despite all the ignoring, all the disrespect, that Charizard is now appreciative of and extremely happy to see Ash, in a way almost identical to its attitude while it was still a Charmander.
The ending of Great Bowls Of Fire. After the Dragonite in the episode calms down, it sees all the destruction it's caused and starts crying. A short time later, all the forest's Pokémon come out to cheer it up.
In the episode Gotta Catch You Later, when Ash and Brock and Misty split up. They declare each other best friends before parting ways.
When it shows their thoughts afterward:
Misty: "Well, Ash Ketchum, finally, I know how you feel about me."
In Why, Why Not!, Bayleef and Noctowl find a Wynaut trying to open a box. Bayleef opens it for the Wynaut revealing some cherries and the badges Team Rocket stole from Ash. Meanwhile Team Rocket is chasing a Wooper thinking it stole the badges they stole from Ash and come face to face with Bayleef. Jessie and James send out their Pokemon to attack, but Bayleef grabs the Wooper and Ash's badges and tries to fight back. Arbok uses Poison Sting, but Wynaut jump and uses Counter (or Mirror Coat) to send the Poison Stings back at Team Rocket. At the end, Ash reclaims all of his badges except for the Rising Badge. Wynaut finds it and gives it to Bayleef and Noctowl. They try to tell Ash that Wynaut is to thank for returning his last badge but unbeknowest to Ash, Wynaut hitches a ride on a boat and waves goodbye to Bayleef and Noctowl.
In Good Quil Hunting, Ash wants to catch a Cyndaquil, but when Team Rocket shows up and starts causing trouble, Ash forgets about catching the Cyndaquil and just wants to keep it safe. Team Rocket shoots giant wads of gum, sticking Ash and Pikachu to a wall. Ash's right hand is free and decides to let go of Cyndaquil and tells it to run. Cyndaquil is reluctant to leave, Ash and Pikachu assure it that they'll be okay. Then when Team Rocket's robot is about to blow up, Ash throws a Pokeball at Cyndaquil not to capture it but to protect it from the explosion.
In Cold as Pryce, Ash and Pryce are knocked off of a cliff because of Team Rocket and due to some quick thinking, Ash uses Noctowl and Totodile to save them from the impact. Due to this, Pryce explains his Ice King tendencies, when he was younger, he had a Piloswine who was badly hurt by a Magmar in a battle and Pryce tried to protect it from a fire attack and got burnt badly and his Piloswine left in the middle of the night and Pryce thought it abandoned him. It turned out that his Piloswine left to find some herbs to help Pryce's burns and was frozen in the snowstorm outside and Ash was able to get Cyndaquil and Pikachu to unfreeze and restart his heart. Thanks to Ash, Pryce got to reunite with his Piloswine and is incredibly happy because of it.
Misty saying goodbye to Togepi after it evolved into Togetic and chose to stay with the rest of its kind. It's one of the show's most emotional scenes ever. Especially the hug.
Misty: Togetic... I love you.
Also counts as one of the series biggest tearjerkers.
A Poached Ego! is a mix of this, Tearjerker and Crowning Moment Of Awesome for Team Rocket. They save a bunch of poached Ekans and Koffing and perform a non lethal Heroic Sacrifice so they can escape and release Arbok and Weezing to make sure the Koffing and Ekans stay safe. Arbok and Weezing reluctantly leave, crying the whole time over saying goodbye to their masters.
May choosing not to capture a Swablu she and her friends nursed back to health, instead helping it catch up with its flock. May is seen trying so hard not to lose it.
The episode Do I Hear A Ralts. In that episode, Max saves a sick Ralts from the brink of death. Once it is better, they have to part, but they promise that they'll be together when Max becomes a trainer. Surprisingly, the music-edit happy 4Kids even managed to write a moving ballad specifically for the dub of the episode (and managed to keep a rarely heard track as well).
The episode Time Warp Heals All Wounds!, when May sees Jonathan and Edna together again. Especially with that 'song'.
Love, Petalburg Style is a mix of this, Crowning Moment of Funny and a bit of a Crowning Moment Of Awesome. It seems that throughout the episode, May and Max's dad Norman is having an affair with Nurse Joy. It turns out that Norman was getting Nurse Joy to help him with a present for his anniversary with Caroline, Max and May's mother.
When everyone crashes on an island, May and Drew accidentally fall in a river and almost go down a waterfall, but are saved by a group of wild Wynaut. Later, the Wynaut offer May and Drew some Lychee berries and invite them to a dance party.
In Strategy Tomorrow Comedy Tonight, the gang meet a girl named Ada and her Chatot. She says that Chatot has recently been flying away and saying strange things and find out that Chatot has been sneaking off to a kid's hospital and making the kids laugh. In return, the kids feed Chatot some cookies.
When they discover that Chatot is at a kids hospital, what's the first thing Ash and company do? They proceed to put on a little show for the kids...which then promptly turns into a Crowning Moment of Funny when the first act is "Takeshi's Paradise"...
James refusing to steal Pokemon from his own grandparents in Sweet Baby James, because they were the only ones who truly loved him when he was a child and also counts as an awesome moment since he helps Ash defeat Jessie and Meowth.
He also spent the whole episode lying to his grandparents saying he was the president of a company. At the end, he decides to come clean about being a Team Rocket member.
In the first episode of the Diamond and Pearl Battle Dimension, Chimchar's Tears/Tears for Fears. In a practice battle between Ash's newly acquired Chimchar and Dawn's Piplup, Chimchar loses and, after getting knocked to the ground, remembers how Paul abandoned it because he considered Chimchar too weak and assumes Ash may do the same or, at the least, believe he's weak as well. When Ash picks Chimchar up, Chimchar looks ready to hear Ash tell it how weak it is, but to its surprise, Ash praises it and commends Chimchar on how hard it tried. Brock and Dawn do as well and the other Pokémon all cheer for Chimchar. Chimchar tears up and throws himself onto Ash's shoulder as he cries his eyes out. Although he doesn't understand until Brock explains, Ash hugs Chimchar and lets him know everything's okay. Even Meowth, who'd gotten separated from Jessie and James and happened to be nearby, was crying and felt sorry for Chimchar.
Ash in English version: Chimchar. It's okay. You're gonna be fine.
Ash in Japanese version: Hikozaru. Cry all you want. It's okay to cry.
In one episode, Chimchar gets poisoned by Saturn's Toxicroak. Ash is very upset, beating himself up over letting Chimchar get hurt like that. Then this◊ happens. It's so incredibly touching, especially in the context of Chimchar's past. It's like he's telling Ash he doesn't have to worry, because he's already done more for it than he could ever imagine.
Crossed with a Moment of Awesome, this trust came to a head in the finale of Ash's full battle with Paul at Lake Acuity. As the last of Ash's Pokémon able to battle, it's given some encouragement after it defeats Paul's Ursaring...which Chimchar replies to by evolving into Monferno.
The ending of the Sinnoh Grand Festival arc. After a real nail-biting battle between Dawn and Zoey, the outcome shows that Zoey has won by one point. And this time, even though Dawn had a brief look of disappointment on her face, she didn't break down and cry, and congratulates Zoey. After changing back into her regular clothes, Dawn meets up with her mom, Ash, and Brock. Dawn's mom was really proud, and is given back her first ribbon by her daughter.
In the episode in which Ash's Turtwig evolves into Grotle, Paul's Torterra proves that Pokémon don't necessarily take after their masters by acting as a mentor to Grotle, who has become disheartened as all of its battling techniques from its Turtwig stage no longer work with its new, heavier body.
Just... Team Rocket rooting for Ash in his battle against Paul.
When Reggie tells Paul's Pokemon he lost to Ash, they are all visibly upset to hear the news. They even rejoice to hear they''ll be training harder than ever when Paul gets home. Whether he shows it or not, Paul must have some connection to his Pokemon despite his reclusive behavior.
Or Crossing Paths. Jessie crushing the Poké Ball to tell Dustox that it was okay to leave, to go off and find happiness.
A much subtler one, but the reaction from Dustox's new partner when Jessie does this. He looks absolutely furious that Jessie made his mate cry.
Ash and Trip's Third Battle shows Trip as a Cheerful Child in a flashback watching in awe as Champion Alder defeats a challenger with his Bouffalant. Afterward, Alder allows Trip to pet and feed Bouffalant, and encourages him to pursue his dream of becoming a Champion. D'awww.
And two episodes later, Iris and Excadrill reconciling.
Made even more heartwarming because we find out that the real reason Excadrill chose to disobey Iris was because he actually cared for her, and because he didn't want to let her down in a battle again. This makes their battle at the end even more of a CMOH than before.
In Oshawott's Lost Scalchop!, Ash's Oshawott gets upset because he's lost his Scalchop in an earlier battle, and he has no way of defending himself in their rematch. Ash (and his friends) go to a huge effort to find a substitution to cheer Oshawott up.
Later, Cilan's Dwebble makes a large stone "Scalchop" for Oshawott to use, but it's too heavy for him to use properly. Because of that, he spends his time training to use the stone Scalchop, not even eating his dinner (considering that he's the group's glutton, that's something). Ash and Pikachu, on finding out, immediately chip in to help Oshawott train using the Scalchop for the entire night, so that he can prepare for the rematch. Finally, at the end, he puts up a successful fight against a Pokemon he has a type disadvantage to, and he collapses in an adorable position, asleep in Ash's arms.
BW077 has Tepig becoming depressed because he feels useless and hated by his old trainer, whom he still likes despite being abandoned. Cue Snivy, of all Mons, coming forward and Vine Whipping him in the cheek to remind him that he is better than he thinks he is, and that he shouldn't be moping about like that. She even goes on to join him in a tag battle that she has an obvious type disadvantage in (Fire and Fire). Though she ends up fainting after defending him from a combined Flare Blitz/Flamethrower attack, it's pretty obvious she was fighting hard to cheer him up and bring him out from his slump. Considering Snivy's regular personality towards her teammates, this is really, really touching coming from her.
She even requests not to go back into her ball so she can watch the end of the match, and when Pignite wins, she happily hugs him along with Ash.
It's not so surprising that Snivy was the one who tried so hard to reassure her friend, here. Besides being the Unova team's Cool Big Sis, she knows what being abandoned by your trainer feels like (albeit her trainer did so because they couldn't raise her), and she was not going to let Tepig's sense of self-worth suffer because of a Jerkass who tied the poor little guy to a pole (with his snout tied shut by the rope). This episode reminds people why Snivy is considered an Ensemble Darkhorse despite not always doing as much as some other Mons.
Seeing all of Ash's Pokemonnote the ones he still owns anyway at Oak's place in the first opening of Best Wishes 2. Yes, even Primeape.
How James gets Yamask in BW023. No battle, no tricks, nothing villainous at all—it's hungry, so he feeds it.
The majority of James' Pokémon were acquired through heartwarming, non-villainous means:
Growlithe: Pet since childhood.
Koffing: Birthday present.
Cacnea: James gives Cacnea a bag of cookies. Confused as to what the bag is, Cacnea tracks down James so it can give the bag back to James. James feeds a cookie to Cacnea, Cacnea enthusiastically (and painfully) hugs James.
Chimecho: Chimecho heals Team Rocket with Heal Bell. James, who has wanted a Chimecho since he was a little boy, politely asks if Chimecho wants to be his Pokémon. Chimecho accepts right there and then, hugging James' face for good measure.
Mime Jr.: Deliberately activates the mechanism on an empty Poké Ball that James accidentally dropped on the floor. Mime Jr.'s former caretakers specifically point out that it did so because it liked James and thought he was a kind person.
Carnivine: He saves it from drowning in a giant pool of mud as a child and it waits inside its Poké Ball for years until they could be reunited again.
Even with Victreebel, chomping on his head was just its way of showing him affection.
When Charizard returns for the first time in quite a while, he and Ash share a fistbump◊ after the obligatory Flamethrower greeting.
The series of flashbacks Ash has of his time with Charizard are a meta example: even though we may never see Primeape or Pidgeot again, seeing them animated in the new style was pretty heartwarming. They've been gone from the show for over 12 years, after all.
The Best Wishes Decolora Adventure! Ending theme is as heartwarming as it is nostalgic: Close to the end, there's an amazing shot of Ash's friends and rivals and their Pokémon seen thoughout the anime and all of them are holding hands: Paul, Gary, Tracey, Dawn, Iris, Ash, Cilan, Brock, May, Max, Misty, Virgil, Trip, Cameron, Stephan, Bianca, Burgundy and Georgia. Then there's another shot of them all along with Delia, Professor Oak, Shannon, Luke, Chili and Cress, along with practically every Pokémon that had an important role in the anime's run. Incredible really...
We also see the main characters keeping in touch with their families as they travel.
During Dawn's reunion with the main cast, Buneary is visibly overjoyed to see an embarrassed but not unhappy Pikachu again.
Professor Sycamore's Garchomp was full of this (when she wasn't Brainwashed and Crazy anyway), from her clear concern over Froakie's condition to allowing Ash and Bonnie to pet her.
Clemont saving Ash after he falls to his life from the Prism Tower.
Ash jumping to (almost) certain death from the top of the tower after Pikachu.
Bunnelby twitching in its Pokeball to acknowledge Clemont's thanks after the heroes defeat Team Rocket, and Clemont's smile in response.
The group-shout in the third episode between Ash, Clemont, Bonnie, Pikachu, and Froakie.
Expanding on this, Ash and Clemont actually lowered themselves to include Bonnie, and so far, from just three episodes, Bonnie is actually treated equally, instead of just as a little kid that's tagged along.
Froakie disobeying Ash's orders and preventing Pikachu from battling Fletchling because he wanted to get payback on Fletchling for making Bonnie cry. When they find out that why Froakie did it, Bonnie thanks Froakie and gives him a hug which makes him blush.
In the following episode, Bonnie is practicing her caretaking skills by brushing Pikachu (who absolutely adores it and lets Bonnie pet his tail), then she asks Fletchling about grooming its wings. Fletchling (who had teased Bonnie the previous episode and was basically a Jerkass), has no problem hopping up and letting Bonnie clean him...he even chirps at her in thanks afterwards!
Clemont grabbing onto Bonnie in the second episode after she grabs his clothing.
Serena's Fennekin protecting its trainer from a wild Vespiquen, and later giving her back her dropped hat.
In XY006, Bonnie is about to fall asleep and Clemont, naturally knowing she's tired, decides to leave the battlefield and put Bonnie to bed for the night.
Serena and Ash's relationship is very heartwarming compared to his usual dynamics with his female companions. It helps that their Forgotten First Meeting is of Ash wrapping Serena's scraped knee with his handkerchief and walking her out of the forest. It meant a lot to Serena and she's been absolutely supportive of Ash so far in their journey.
XY009 has plenty of this, from Ash continuing to serve as an inspiration for his companions this season to Clemont reprogramming Citroid to be a more compassionate gym leader at the end. Not to mention Clemont's gym Pokémon being clearly happy to see him even though they are forced to battle against him.
When Ash is trying to give Pangoro its new leaf, Team Rocket order their Pokemon to attack, but Pikachu and Froakie shield him with their attacks despite being tied up by Pumpkaboo's Leech Seed. Afterwards, Fennekin and Chespin do the same thing.
Korrina's bond with Lucario is pretty heartwarming. They were together 24/7 ever since they were children, they shared meals, played, slept in the same bed, and made each other feel good. Whenever they are seperate they become depressed.
When Korrina was alone with Clemont and Pikachu in XY033, Korrina becomes depressed and lonely, Clemont decided to take care of her by, giving her something to eat and drink and even staying up all night, sitting next to her on the cliff while trying to cheer her up.
After Fletchling is rejected by Nami's Talonflame as an opponent, Bonnie sympathizes with it and even inspires it to come up with a strategy that would allow it to defeat Talonflame later on.
In the following episode, Bonnie is separated from the others. When she calls out to the others, only Pikachu can hear her. The two of them fall asleep thanks to a Foongus attacking them with sleep powder. When the others find them, Bonnie is on the other side of a canyon. Trevor comes up with a plan to use some nearby Drifloons and Drifblims as platforms to reach Bonnie on the other side. Ash volunteers to get Bonnie, he easily makes it to Bonnie, but has trouble getting back thanks to a wind. At this point, Pikachu wakes up and sees Ash and Bonnie in danger and being blown off the Drifblim they're currently on. Pikachu jumps off the cliff to grab Ash, who is grabbed by Clemont's mechanical Aipom arm and everyone else is grabbing the cable, pulling Ash and Bonnie up to safety.
XY043 had two, Korrina decides to give up her room for one night just to sleep with Ash and friends, possibly protecting them and keeping them company. Serena helps Gurkinn walk when he eventually becomes exhausted from running.
During the credits of the eighth movie (at least the Japanese version), when we see the supposedly dead Aaron and Lucario (the latter having just revived his faith in the former after spending the entire film thinking he had betrayed him and then proceeded to save the day) reunited in what is presumably some sort of an afterlife, and Lucario gets Aaron to try some chocolate.
The ending credits to the third movie has a brief one, but it's BIG: Molly is playing with a real Teddiursa in some water when her father returns. This is heartwarming enough, but a second later a woman who can only be Molly's mom shows up, and after a brief look of surprise Molly starts to tear up and immediately runs to her. Molly has her family back, which is all she ever wanted.
Earlier in the movie, Charizard is at the Charicific Valley and looks through a window and sees Liza and Charla watching a news report on TV and notices Entei running off with Delia and Ash chasing them. Charizard immediately flies away to help Ash rescue his mom.
When Charizard is battling Entei, Entei knocks Charizard back, who hits Ash causing him to almost fall off a ledge. Brock grabs his hand and is backed up by Misty, Pikachu and even Team Rocket.
Jessie: I'd say "Prepare for trouble", but you're kind of already in it.
In The Rise of Darkrai, Darkrai itself has many of these, mostly in the third act. Yes, a Pokémon of the same species that hordes the Nightmare Fuel page, has a slightly creepy/sinister soundtrack accompanying it in the movie often, and creates nightmares has multiple Heartwarming Moments. There's a good chance you'll want to hug it and even cry for it by the end.
The farewell scene between May and Manaphy in the ninth movie.
More like the entire movie especially May and Manaphy's bonding and "I love you" scenes.
The plot twist of Destiny Deoxys. We're talking about Deoxys, a tentacled, transforming, regenerating, self-duplicating alien Pokémon here. In the movie, it spends four years regenerating under the ice of the north pole after getting blasted by Rayquaza, short-ciruits all the technology in the city and surrounds it in an inescapable forcefield, and holds pretty much the entire city's population hostage with an army of clones. And it turns out it's doing all this all because it just wants its friend back.
When Zorua finally reunites with her Zoroark in the end of their Movie. Knowing what they have been through they surely deserved it.
Pokemon Black and White Movie: Seeing Victini by the sea which he had hoped to see. Knowing that he is free to go wherever he wants.
From the games, any Pokémon that evolves by friendship. After taking care of it for so long, it likes you enough to evolve from pure happiness.
Take a max-happiness Pokémon to Dr. Footstep and he'll tell you your 'mon's innermost feelings about you. They're usually quite touching and cute, especially if it's a "scary" Pokémon (like a Haunter or a Darkrai), or a "slow" Pokémon (like a Bibarel) that's grown sufficiently fond of you.
Most Pokémon: "<Name> is...a remarkable human and Trainer. That I can always perform the best any <Pokémon species> possibly can...I attribute that entirely to my partner <name>. When we travel, I can see wild Pokémon eying us enviously..." Scary Pokémon: "There are no Pokémon that dislike humans... Only humans that dislike Pokémon... We <Pokémon species> are especially shunned... But <name> always treats me as a friend and partner..." Slow Pokémon: "Hnurrr... Me? Uhm... Other Pokémon, they say to me... "You're not thinking, are you?" How insulting they should say so. It isn't true what they say. Think, think, think, I do that. All the time, I think hard how to help <name>. I concentrate! Hnurrr..."
Other Pokémon: "If I said there can be friendship between Pokémon and people, will <Pokémon species>'s friends understand? But if you see <Name> and <Pokémon species>, you will understand. Because <name> and <Pokémon species> are friends!"
Also in HeartGold and SoulSilver, when you interact with your walking Pokémon and it shows it wants to play or cuddle with you or is even happy just walking beside you.
Ruby/Sapphire/Emerald managed to get in one good moment, namely the sequence at the very end. After you defeat the Champion and talk for a moment, Brendan/May suddenly runs into the room, saying that they want to give the player some advice, unaware that they've already won. He/she then tries to follow you into the next room, and when told that they can't, he/she responds with a very long pause before saying something like, "...If it's the rule, it can't be helped. Congratulations, [name]!".
The surprisingly poignant credits sequence enhances the effect (particularly the music).
In Platinum, your rival is dejected after a crushing loss to Jupiter. However, he exacts his revenge when he arrives at Spear Pillar to accompany you in a double battle against Mars and Jupiter. After the battle, he heals your Pokémon.
The "Return" move is basically your mons saying "This is how happy I am to be with you!" in the form of an attack. When you think about it, it's kind of touching when it comes out at maximum power and KOs your opponent in one hit.
Another one from the third generation—or at least Emerald: after you beat the Elite Four, you can rematch Gym Leaders. After you defeat your father in Petalburg Gym for the second time, the general theme of his lines is that he's So Proud of You.
Norman: "<Name>...what is your dream? My dream...hah. It has already come true, actually." (Then, if you call him on the Pokénav): "You astound me, <name>...how much higher will you soar?"
In Emerald, if you play as May, Brendan will call you once and Ship Tease you when he's talking about Rayquaza.
A precious one from Gen V. When the player reaches Route 7, their mother calls. Not for any plot relevance or to deliver an item, but solely to reaffirm that the player character's mother loves them and is so proud of them. It feels just like a real life mother conveyed in simple pixels and polygons. D'awwww.
Anytime any of your Pokémon do something great, like beating a powerful Pokémon on their own, or winning a Pokéathelon or Contest, or winning a Gym battle, or beating a member of the Elite Four... there's all kinds of stuff they can do that gives you a warm fuzzy feeling.
In X and Y, if you've maxed out your affection with your Pokemon, they love you so much that they can: endure a hit that would've taken them out, shake off a negative status effect, or even have a higher chance of critical hits (though that one can be an problem if you're actually trying to catch the enemy Pokemon).
In X and Y, at the ending, AZ finally is reunited with Floette. His reaction to this is beautiful.
In X and Y, there is an old man in a building in Anistar city. He tells the player that his wife has passed away and asks for a low level Pokemon to keep him company. If you give him one and come back to the house after you defeat the Elite 4, you will find a pokeball with the Pokemon you gave him, along with a letter stating that that he has passed away and he thanks you for helping him in his last moments.
Volume Five of Pokémon: Diamond and Pearl Adventure has Cyrus manipulating Hareta to the extent that one of Hareta's friends (a pawn in the plan) tries to kill herself. When Cyrus gives his evil tirade, he explains that the only true emotions of humanity are "hatred, jealousy, and burning anger", and gloats when Hareta unleashes fury against Saturn's Rhyperior. He caps off his speech with "You must hate me even more now." Hareta's reaction? SOBBING. He tells Cyrus "You do bad things, but I don't hate you," and talks about how he still wants them to battle someday. Cyrus is in disbelief and is nearly overcome, starting to save Hareta from the explosions (the building is blowing up around them them the whole time). Saturn stops him from going back in, but Cyrus leaves a Master Ball for Hareta just the same. Later, it's revealed that even though he got to the Spear Pillar first, Cyrus waited several hours for Hareta to show up. That reawakened human side is key in Cyrus's redemption in later volumes.
Some extra Team Rocket Heartwarming (they sure do it a lot): In one episode, James nearly gets himself killed by trying to capture a rare and powerful Pokémon on his own, and while Jessie comes to rescue him, they both end up getting trapped by the raging Pokémon. Resigned to the fact that they're going to die, Jessie tells James that, if there's an afterlife, she wants to meet him again there. This actually makes the terrified James smile, knowing that he and his best friend won't separate even in death. Luckily, they end up getting saved by Meowth, but still.
Even sweeter because Meowth and Jessie, discouraged by their bad luck, had just abandoned James to go pursue careers. He was extremely upset, but as soon as they found out he was in trouble they ran to rescue him. Then they teamed up again. Status Quo Is God, but still, awww.
Anything where Pikachu almost dies and Ash saves him and they end up hugging.
Meta example from Bulbapedia: "Today is Monday February 27, 2012 - Anniversary edition: Welcome to the World of Pokémon - In celebration of the anniversary, all Generation I Pokémon species articles will feature their artwork from Red and Green Versions." To all of those of us tropers who grew up in The Nineties, the sheer amount of Nostalgia Filter cranks the "heartwarming" part up several notches.
In a special episode starring Brock, a shot of his room shows several photos of all his previous traveling companions◊. In a meta sense it also really shows just how long he's been on the anime, even if he received relatively little focus in spite of it.
On a video of "Emotion" from B/W, a YouTube commentator (by the username JTpiano24) commented about what Pokemon taught him. He said that Red taught him to not fear adventure, Gold taught him to not be afraid of change, Ruby taught him to not tamper with nature and let it run its course, Diamond taught him to not use religion to rule over others, and lastly, B/W taught him that beings had emotions, and that people needed to accept others to achieve peace.
This◊ series of cards from the TCG showing a Tepig growing along with his owner and their family.
These◊ Natu and Bouffalant cards which tell a story of their own.
This comic titled "It's The Thought That Counts which is about a Quilladin who has a crush on a female Braixen. The idea of this sounds cute, but each attempt to charm her doesn't go well for him. But the real heartwarming moment of the comic is how it ends.