Meowth's backstory is sadder than sad, learning to talk, fighting a Persian that's equivalent to a gang boss, all just to impress a female Meowth.
And after all that, she still rejects poor Meowth. No wonder he's such a sourpuss (no pun intended).
Even before he could talk, when he first opened his eyes, he woke up all alone, abandoned with no parents or anything. In the rain even. No pet/animal deserves that.
To make things worse, some humans tied him to a tree for no reason and laughed at him. He even cried himself to sleep.
Later on in one of the Orange Islands episodes (Meowth Rules), he at one point laments; "I should'a known I was never meant to be happy. I don't deserve to be."
While we're on the subject, what about Jessie? Her mother, who she loved more than anything was killed in an avalanche and she had to spend her whole life being bullied and stepped on. All she wants is to be loved and cared about. Is that too much to ask?
In Mystery at the Lighthouse, a gigantic Dragonite is lonely and desperate for friends. It comes to Pokéemon researcher Bill's Lighthouse in the hopes of making one, but is driven off by a terrified Team Rocket. It moans sadly and disappears back into the fog, never to be seen again, with none of the other characters realizing what it was and why it was at the lighthouse.
The Song of Jigglypuff, the song itself.
In episode three of the original series, Misty's fear of Caterpie drives it to return to its Poké Ball. The way it does so is a slow sad walk.
Sabrina's (the Saffron Gym Leader) backstory of how she discovered her psychic abilities as a child and used them to wreak havoc on her parents (causing her father to run away and her mother to incur the wrath of her daughter's powers by being turned into a doll), then became so powerful and obsessed with honing her abilities that the innocent, childlike side of her that wanted to play and be a kid split from her mind and manifested itself into a doll. It took Haunter's goofy antics to make Sabrina regain her humanity for the first time in ages.
The end of the Indigo Conference arc. Watching a recap of Ash's entire experience of all the battles he went through, all to the glorious sound of the Pokémon Theme. It makes you feel like he really did give his all to get as far as he did. You feel proud that he did so well. And afterwards he stands in the middle of the stadium, and reasserts his vow to become a Pokémon Master. The Pokémon League may be over for Ash, but his journey has only just really begun.
The climax to the first episode, Pokémon - I Choose You! Try not to get a knot on your throat when you see Ash eager to be pecked to death for an insubordinate Pokémon he only just met.
The Kangaskhan Kid. The titular Kangaskhan kid is a young boy who was dropped in the Safari Zone when he was a toddler. His parents frantically searched for him, but they were unsuccessful for years. When they finally reunite with him, he doesn't recognize them at all. He's also declared himself the protector of the Kangaskhan, which puts him in a dangerous situation with Team Rocket. To protect their long-lost son, his parents fly their helicopter into Team Rocket's vehicle, which seemingly kills them. The boy, now accepting the truth about his origins, weeps over his parents' "death." Don't worry, all turns well in the end.
For some, it's not so much the episode as the song "The Time Has Come (Pikachu's Goodbye)" from the Image Song CD. You can listen to the song here, if you don't mind tearing up.
If it was even possible, 4Kids did manage to make the first two even sadder than it was originally (the dub opening was surprisingly effective in making Butterfree's departure dramatic). Pikachu's Goodbye also had a Heartwarming Moment at the end of the episode.
Butterfree's goodbye was recycled ten seasons later with Jessie's Dustox. Didn't have the music making it sadder, though, the way Bye Bye Butterfree is.
The original has the first movie's theme, "Kaze to Issho ni" (Together With the Wind), playing over the release. And let's face it — it's the first time Jessie's broken down like this. Watching her crush Dustox's Poké Ball under her foot in tears is heartbreaking, and a rare soft moment from the Team Rocket trio's leader.
Season 11 was a very emotional season for Team Rocket. In the second episode, "Once There Were Greenfields", James surrendered Cacnea to a gym leader, Gardenia, because he recognized he could not teach Cacnea to master Drain Punch. In its final match, where Ash agreed to have Aipom fight Cacnea. It tried so hard to do Drain Punch, even though its determination to master the move led to it getting kicked to the beat. So badly, its futile determination wiped the smile off Aipom's face.
Meowth after losing the battle to get Togepi in EP050. At least he wasn't dealt the further embarrassment of being sent blasting off, the sobbing Pokémon instead dragged off by Jessie and James.
Meowth: Little Togepi... I hope you'll be very happy with your new trainer... Goodbye now...
The entire first episode of Charmander's appearance. Just picturing it freezing and shivering alone on that rock during the rain storm doing its best to prevent its tail flame from going out, and essentially killing it is one of the saddest moment of the series.
The end of "Charizard's Burning Ambition" was heartbreaking, because the way Ash left Charizard said, "If I stop, I'll change my mind."
Charmander's story in general is quite sad, though it does get better. It was good friends with Ash, but when it evolved, it suddenly became hostile and aggressive, which got worse when it evolved into Charizard. However, at one point, it is weakened during a battle, and Ash spends the entire night trying to keep it warm, getting blisters all over his hands in the process. The next day, for the first time, Charizard fought for Ash.
The beginning of the episode "Gotta Catch You Later" where Ash, Misty, and Brock separate after being together for so long is pretty moving.
The farewell of Misty in the Master Quest season.
Everything about that first half of the episode. Misty's sad look when she realizes she'll have to go home. How upset she is when Ash, not realizing the gravity of the situation, just comments that she has her bike back and can get home faster...then her walking away crying, thinking that Ash doesn't seem to care that they have to split up. Then Ash and Brock show up to help her battle Team Rocket...Ash compliments her on her battling and Misty, instead of brushing it off like usual, thanks Ash and says it's "sweet" of him to say. About the only thing the dub missed was the fact that in the original, Misty tells the eternally-dense Ash, point-blank, that "it was never about the bike".
Misty: One more thing...
Ash: That's enough...
Misty: It's just something that I feel I need to tell you...
Ash: All right...
Misty: Just keep on...doing your best...
Ash: Uhh...what do you mean?
Misty: Well...you know...without me there...
It was also the last time the original cast traveled together. In the Kanto Battle Frontier, May and Max were with them, and Misty never rejoined Ash and Brock alone, and with Brock having been Put on a Bus after Diamond and Pearl, they likely will never reunite for another adventure. The Fellowship Has Ended indeed.
In general, the group (whoever they may be) inevitably going their separate ways at the end of each saga tends to be a fairly emotional affair.
Larvitar's backstory in "Address Unown". The poor little mon can do nothing but watch in its egg as its Tyranitar mother is injured by the poachers who kidnapped it, leading it to be afraid of humans when it hatched. And later on the memories are too much for it, represented by Larvitar essentially being frozen in an ice crystal. It's followed by what is considered to be for some, one of Ash's biggest Moment of Awesome: his heartwretching "I Know You Are in There Somewhere" Fight to Larvitar.
Speaking of James, most people still can't get through the episode 'Holy Matrimony' without bawling like a little kid. James is telling the story of what happened to him when he froze to death as a child after running away from home, with his Growlithe watching helplessly at his side (the fact that it is still fake doesn't make it any less sad) is already tear-worthy, but at the end when he's forced to leave Growlie so he can rejoin the villainous Team Rocket and remain a free man is part heartwarming, part tear-jerking.
In a certain Johto episode, Team Rocket locks up Chikorita in a strong cage, making her unable to escape with Razor Leaf or any other maneuver. Team Rocket then proceeds to use its Pokemon to attack Ash. Chikorita is forced to watch her master, who she undyingly loves, be harassed without the ability to stop it. You can even see her eyes well up with tears. She evolves into Bayleef in time to save him, but it's still heartbreaking to watch.
The very next episode has poor Bayleef trying to show Ash affection the way she did as Chikorita twice and ending up tackling him without meaning to, making Ash arguably the angriest he's ever been in the show. Just before lunch, when she's calmly walking towards him specifically to avoid tackling him to the ground, Ash yells at her to get away andstayaway from him. (Misty later calls him on this, and Ash realizes that he made an awful mistake.) The look on Bayleef's face is heartbreaking even if you dislike her for her Clingy Jealous Girl tenancies.
In the Orange Islands episode "The Mystery Menace", Ash's Bulbasaur and and Misty's Togepi are kidnapped by a mysterious monster living in the sewers. The monster turns out to be a Bulbasaur feeling lonely, after having been abandoned by its original owner decades ago.
Just a small one from "A Scare in the Air," watching Jessie and James sit there mumbling "Looks like Team Rocket's messing up again."
"A Poached Ego" gave us Team Rocket's Moment of Awesome at the cost of a few tears. TR comes across a poacher who has captured a bunch of wild Ekans and Koffing, the pre-evolutions of their main Pokémon: Arbok and Weezing. In an Even Evil Has Standards moment, TR attempts to free the captured Pokémon, but the poacher tries to stop them. In the climax of the episode, Meowth manages to free the Ekans and Koffing from their cages. When the poacher sends his Tyranitar after them, all three Rockets throw themselves at it. The battle is completely one-sided as the Tyranitar beats them mercilessly, all while Jessie and James are shouting at Arbok and Weezing to take the Ekans and Koffing and run far away.
The look Arbok and Weezing have on their faces shows that they'd clearly like nothing more than to go back and battle to protect their masters. But just as they always had for the entire series to that point, they obeyed that final order.
"Go West, Young Meowth". Meowth's backstory is indeed a sad one. He learns to speak human language, and goes through all sorts of ordeals in order to walk like a human, just to impress a girl of his species and the pet of a rich woman... only for her to reject him. Then there's the end of the episode, where Meowth stares at the moon still pining over Meowzie.
Then, if you still aren't moved by all the emotional moments Meowth goes through in the first parts of the episode, wait until you see what follows. Meowth meets Meowzie again in an Dickensesque pauper gang, and the viewer learns that her rich, loving owner set her loose when she lost all her money.
When Lapras finds its family again, but they shun it because Lapras is with humans.
The first episode with Lapras being abused also counts for this trope.
In the episode "Great Bowls of Fire", Dragonite snapping out of its Outrage only to witness the results of its attacks: the complete destruction of its peaceful forest home. Its tearful howls are pretty heartbreaking.
Squirtle leaving Ash and rejoining the Squirtle Squad.
Probably one of the most overlooked moments in the entire series would have to be when Pidgeotto (now Pidgeot) leaves Ash to protect some wild Pidgey and Pidgeotto from a gang of Spearow led by a Fearow who evolved from the Spearow that Ash tried to catch on the very first day of his journey.
And then made even more sad by the fact that Pidgeot doesn't just leave. Ash makes it out as though it's a temporary arrangement, tells Pidgeot that he'll be back after Professor Oak's pokeball has been delivered, and waves it off cheerfully, calling out that he'll see it soon. He never comes back.
The "Fly Me to the Moon" episode. Period. Ash & co. find a trainer with a Pidgey called Orville, who is the only one in the entire island who can fly. He wants to fly in the sky higher than any other Pidgey did, and reach outer space. Ash & friends (and more importantly, Team Rocket) help him, and obviously he achieves his goal...But when he reaches the atmosphere, he's already freezing, and without oxygen, on the verge of death....Meowth, who is translating what Orville says through a communicator, says that Orville told "he has never seen something so beautiful" when he sees the Sun from the atmosphere. Meowth then pleads to Orville to get back to Earth before it's too late, and the Pidgey falls from the skies in an unconscious dive.....He gets better, of course, but to see the self-sacrifice of the Pidgey to achieve his dream almost reducing even Meowth to tears was...oh dammit...
Meowth's pep talk the night before Orville takes flight.
Meowth: It's okay, pal. Meowth is here to help ya! Once upon a time, Orville, I was just like you. I yearned. I yearned to rise above other Meowths. Nothin' was ever gonna stand in my way to learn to talk human talk. Y'see where I'm goin' with this?
Meowth: I understand what you're goin' through, pal, and I wanna help you, cause nobody was there to help me. So I'm gonna be flyin' alongside ya, as far as this here balloon is able to take me. And with this mini micro walkie-talkie, I'll still be able to stay in communicato with ya. ...This is too important to blow! Pokemon need to hear this! You will be a hero! When they see what we're capable of, all Pokemon, big and small, will make their own dreams come true!
Meowth: For the Pokemon!
For extra points, the English script was actually written by Maddie Blaustein, Meowth's voice actress.
For added meta-subtext, Maddie Blaustein, when talking with the fandom online, had directly compared Meowth's past to her own life as a trans-woman. This adds a new layer to Meowth's original past, his conversation about "focusing on being the same instead of being different" in the first movie, and Meowth bringing up his past in this episode.
In the Johto episode "Forest Grumps", Jessie (who is sleeping in a cave with Ash and Brock) remembers talking with a woman when she was a child, telling her she wanted to be a Trainer and a celebrity when she grew up. The woman tells little Jessie, "It sounds like you're going to have a very interesting life!" The sad part kicks in with Jessie's realization that her time on Team Rocket is miserable and not anything like what she dreamed.
Before this episode, Jessie met up with a Blissey she knew in school. It then goes to a flashback of her when she was even younger, and wanting to apply to become a Pokemon nurse. She did "not meet the requirements" to become a nurse. But you then see she did very well at taking care of the Pokemon, and it seems it's implied it was because she didn't look like a Nurse Joy.
In the Kanto episode "The Kangaskhan Kid", a mother and father search for their son Tommy who was lost at 3 years old, only to have Ash & co. find him at the Safari Zone living amongst the Kangaskhan a la Tarzan. Near the end of the episode, Tommy's parents help foil Team Rocket's plans via Heroic Sacrifice and afterwards, Tommy starts bawling his eyes out, thinking both of his parents are dead. It's revealed however that both of Tommy's parents survived the attack and tell Tommy that they will both live with Tommy and the Kangaskhan. The family is reunited once more.
'Lights! Camera! Pika!' is an episode about an old man named Frank, who loved Pikachu ever since he was a kid. You can can say that he was a Pikachu fanatic, since got married to a woman with Pikachu gathered around them, but keep in mind that he only had his granddaughter when Ash and co. met him. The sad thing is that in that flashback, Frank is grieving on a tombstone, implying that his wife passed away.
In the aforementioned "Ignorance Is Blissey", a Blissey from Jessie's nursing school gives Team Rocket her entire center's worth of food out of the joy of seeing her friend again. When this rather overzealous act of kindness gets Blissy into trouble with her boss, Team Rocket decide to take the fall for her and pretend to have mugged her for the food, inevitably setting themselves up for a good beating from the heroes. The even sadder part is Jessie constantly having to stop Blissy from intervening and revealing the whole plan throughout.
In "Mending A Broken Spirit", James is touched by a situation Serena's Braixen is undergoing (its branch broke and the trainers aren't understanding her attachment to it and why it's having trouble performing properly). He takes the alias of "Jeeves" and explains the situation to Serena, helping her solve the problem with her Pokemon. After James is unwillingly drafted back into Team Rocket's new scheme, the heroes angrily blast him off with the others, ignoring his happiness over Braixen's regained power. To add onto this, Serena later concernedly asks where Jeeves is.
Whenever one of the team considers ditching Team Rocket to go to bigger and brighter things, but being unable to part from their friends, and thus staying on in their loser position. It's especially tragic since all three of them (and more counting some of their Pokemon) have been through this, though ironically they still end up holding each other from any better calling. In some cases they even beg one of them to take their chance and defect.
James being forced by Jessie and Meowth to trade away his Victreebel for a Weepinbell in "Here's Looking at You, Elekid!" He just seemed completely and utterly distraught by losing his beloved Pokémon, and then later in the episode when his new Weepinbell evolved into a new Victreebel, Jessie sends the Pokémon flying, never to be seen again.
Misty releasing Togetic in "A Togepi Mirage." Especially when you think of it from the standpoint of Misty being a mother that has watched her 'child' be born, grow up, and then reaches the moment where she has to let go and release that child into the world to live independently of her.
Misty: Togetic... I love you.
For some, it's James' farewell to Chimecho, especially his line in the dub: "It's just...I don't know how to deal with this!" Some of the same people also tear up every time they see May tearing up after losing the Kanto Grand Festival.
Odd Pokemon Out! has Grovyle falling in love with a Meganium after the latter heals him after he lost his battle with a Tropius. Grovyle goes off to fight Tropius again, this time defeating it, and spots Meganium running towards him. He expects that she was going to congratulate him... but she doesn't. She runs straight past him to Tropius, heals him, and then nuzzles up to him, which was when Grovyle found out that Meganium never loved him, but she loved the one that kicked his ass earlier. Ouch.
And not too long after that, he evolves into Sceptile, only to be unable to use any of his moves. It was a real kick in the face watching Team Rocket's Pokemon knocking him around like it was nothing.
In "True Blue Swablu", near the end when just as Swablu is about to join May's team on her journey, its family comes back. The music, May desperately trying not to break down and Max's questions about why she's letting Swablu go back to its family despite it wanting to come with their group in the first place.
"Do I Hear A Ralts?" Plot: Max finds a sick baby Ralts by the side of the lake. He has to take it to a Pokémon Center but several things are getting in his way, including Team Rocket, the severity of the fever, and the distance to the Center...but he clears all the barriers and manages to get Ralts to the Pokémon Center without knowing if it will live. The next day, it is completely cured, but has to be returned to its family, Kirlia and Gardevoir. Ralts does not want to leave Max, telepathically telling him to promise that he'll come back for it when he's a Trainer, and Ralts teleports away as the episode ends.
Insert in there one of the most genuinely touching sibling moments in any anime. After Max gets to the Pokémon Center, as Nurse Joy works on Ralts, the other twerps arrive. Max breaks down and runs crying to May. She consoles him, and expresses her pride that he had saved Ralts.
While Maxs crying over his father losing to Ash veers into wangst-territory due to him overreacting, his Broken Pedestal can come off as tear jerking. Max seen his father as his idol, someone who is perfect and can never lose or make mistakes. Seeing his father lose and not showing any sadness about it must have triggered Max into getting upset and taking Ashs badge away, due to being in denial of his father losing. This also may be the implied reason as to why Norman doesnt allow his kids to watch his gym battle. Thankfully, everyone gets Max to face reality and realize that losing is a part of being a gym leader.
The send off episode with May, Max, and Brock is also sad. Max is crushed the most and revealed about how hes jealous of May traveling due to him not wanting to go back home. You cant help but feel sorry for the kid.
The entire "Team Shocker!" episode is a huge tear jerker. Dawn, the resident cutie is broken all of a sudden, after 2 lost appeals. Soon after, it cuts to a scene where her mom Joanna is shown disappointedly glancing at a wall full of photos of both her and daughter participating in contests. Next, Jessie goes and rubs her victory in Dawn's face! And Dawn later cries herself to sleep..
It was so upsetting that Ash himself was on the exact same emotional wavelength.
The first time she loses the appeal round is pretty bad too, as Dawn runs outside and bursts into tears. It's also the very first time it has ever happened. The Skyward Scream she lets out when the others unsuccessfully try to get her back doesn't help in the slightest.
In a fight against Team Galactic, Saturn's Toxicroak attacks Pikachu with Poison Jab, but Chimchar takes the hit for him and ends up poisoned and badly injured to the point that he can't fight anymore and Team Galactic escapes. As Chimchar recovers, Ash takes it badly, blaming himself for his Pokémon's wounds.
After Turtwig evolves into Grotle, he realizes that his new larger and much heavier body hindered his mobility, and after being defeated by Paul's Honchkrow and recovering at the Pokémon Center, he leaves on his own to train in a desperate attempt to improve his speed, to no avail. After a few failed attempts in which he trips, falls on his back and hurts himself, Grotle is shown about to cry.
The part when Ash had that crushing loss to Paul — the fact that Chimchar evolved into Monferno and tried so hard to pull another win for Ash and the fact that for the last bit of that episode you do not see Ash's eyes at all...
And then the next episode... Ash's in a depression. Not only has Paul defeated his pokemon, but his philosophy and beliefs in what brings out a strong pokemon. He has to watch all of his Pokémon get treated, then lays on the side of the hill, remembering the battle over and over and over. He was in a depression for a good 25 minutes of the episode! Not even GARY beat him that hard. Thank goodness his friends cheered him right back up, and good thing it was soon, because Team Rocket tried to insult him AFTER he recovered.
James having to give up Cacnea so it can learn Drain Punch. Sure it was a Team Rocket Pokémon that was often used as a punching bag for the protagonists, but you can't really help but root for the cactus Pokémon in his departure episode. Watching it being battered while trying to master Drain Punch can make some people tear up.
The end of the Team Galactic arc. Saturn has remained his usual, cold, fierce self, but then stops Mars from going into the portal; and at the end when they're taken away, the fact that Mars, who had previously been extremely spring-loaded, occasionally bordering on annoyingly insane, was just so quiet and didn't put anything in to the conversation. Of course, that scene turned (sort of) into Nightmare Fuel with how coldly and fiercely Saturn tells Jupiter that Cyrus got away.
If you know (and sympathise with) Cyrus' backstory and believe it applies in the anime universe (the verdict's out on whether it does or doesn't), then it becomes even worse.
Mars' reaction when Cyrus tells her he'll be the only one in his perfect world. Once she puts two and two together, the way she screams and then she runs after him as the portal's closing. Saturn stops her from going in after him.
In DP074, Pikachu takes a Hyper Beam from a Raichu at point-blank range, and almost dies. All Ash (and Team Rocket) can do is watch desperately from behind a glass window.
The final episode of the Diamond-Pearl series, "Memories are Made of Bliss!". Brief summary: " Ash, Dawn and Brock arrive back in Twinleaf Town, and while waiting for a ferry back to Kanto the gang become depressed knowing they'll soon be going their separate ways. While everyone tries to keep their sadness at bay, it proves to be too much for Piplup..." Piplup takes it very badly. Since the party just can't move from a region to another without splitting, there is no way this is gonna end well.
Piplup breaking down in front of Pikachu...indeed; the realization of leaving one of his best Pokémon friends became too much for Pikachu as well, and the Team Mom Togekiss has to comfort them both.
And while that's happening, this music plays, which in and of itself is a bit of a tear jerker for fans of the old seasons.
And if you watch the Japanese version, you see this tribute during the ending credits. It's a simple, but beautiful sequence which farewells Dawn and Brock from the regular series and reaffirms the series' themes of friendship. The song playing, In Your Heart, Lalala, itself counts as a major tearjerker, especially if you know the lyrics.
We hear a lot of Paul's treatment of Chimchar, but remember Paul's crushing defeat by Brandon. When he heard that Ash defeated Brandon, Paul was in shock, even his brother was never able to defeat him, but Ash, the one trainer who at this point, never came close to beating Paul, did. Paul was in his absolute best against Brandon, and while Brandon did take the fight seriously, he defeated Paul with total ease. It is also the fight that we see why Paul is the way he is. He was there when Reggie lost to Brandon, and it's here that he decided that power was the only way to win battles, and to his credit, he got results and became an exceptional trainer. Just to see him lose one pokemon after another, losing his cool in the process, only for it to come down to his Magmar going up against Regirock, the battle was already over. Just to see Paul, the most powerful rival Ash has ever met by this point, being backed up to a corner and lose, especially with the background music, you feel nothing but pity for him, coming in demanding a fight, only to basically be put in his place. He at least took his defeat with stride.
Tepig's background story is just as bad. After Tepig loses a battle, his trainer abandons him in a rather cruel way; the porker is tied to a fencepost and forced to watch his trainer walk away on him. To make matters worse, he still loves his trainer; Tepig literally breaks down into tears and tries to chase after the guy. Before Don George can free him, however, Tepig shoddily bites through the rope and promptly sets off to find said ex-trainer. Oh, and some of the rope gets caught around his snout. When Ash finds him, Tepig is on the verge of starving to death.
Another sad thing is that Tepig still had some issues to overcome after it was abandoned. When it would win battles, Tepig would be overjoyed. When it lost battles, however, it would become sad due to fear of being abandoned. Thankfully, Tepig overcame this problem when it evolved into Pignite.
Ash and Iris arguing in the episode The Path That Leads To Goodbye. Their arguments started over petty mistakes the two unintentionally made towards each other, and you can see Pikachu and Axew desperately trying to get their respective trainers to calm down. The argument gets so serious to the point that Iris calls off her friendship with Ash.
Iris's backstory is basically a long Break the Cutie: after meeting Drayden and being spirited away to Opelucid City to get an education, she quickly finds out that she doesn't fit in with the more sophisticated city-dwellers, and does poorly in a school environment. (It's also implied by her issues with books that she may have been near-illiterate, or at least very unfamiliar with books.) She grew despondent and made no friends, and would often run away to hide at the top of a tower to be alone. She eventually couldn't handle the city life and went back home. In the series proper, her return to Opelucid City treats her to bittersweet memories.
While Iris and Cilans send off episode wasnt as tear jerking as the other send offs, what makes it sad is that you never see the two appear again in the series (apart from their Japanese-exclusive episodes).
When it seems as though Dragonite finally decided to obey Iris in the latters match with Ash, it stops doing so after Ashs Krokorok evolved into Krookodile. Dragonite again loses faith in not only Iris as a trainer, but itself, which led to it throwing a massive tantrum and it suffering a humiliating loss to Ashs Krookodile. After the humiliating defeat, Iris wasnt in the mood to get into her usual petty squabbles with Georgia when the latter revels in Iris demise. Iris even wonders what went so wrong that Dragonite just decided to disobey her out of nowhere again, only for Cynthia to tell Iris that Dragonite doesnt have much faith in her as a trainer. After this, Iris takes her loss in stride vows to become a better dragon trainer for her dragon Pokemon.
Bianca's reaction to losing to Cameron in BW104. It was obvious how excited she was at being able to compete in the Unova League tournament, and to have all of that taken away from her so quickly... It really doesn't help that this is the first time we've ever seen her actually cry on-screen, not just have tears well up in her eyes, especially considering how upbeat and cheerful she is normally. Luckily she gets over it, but still...
The Junior Cup arc has a lot of minor tearjerkers: Caitlin has a moment of doubt in her abilities up against Cynthia (which is a bit more melancholy if you take her backstory in the games into account), Trip loses to Alder and is genuinely frustrated and disappointed, having worked hard to get there, and Dawn departs Ash's company for the second time.
A minor one in Best Wishes when Dawn leaves Unova after the Junior Cup. Piplup is about to say goodbye to Meloetta, when Oshawott pops out. They confront each other tensely, then both tear up, and they hug each other sadly. They'd spent eight episodes at each other's throats over Meloetta, and it's like they realized they wasted their time on something silly and missed a great opportunity to truly be friends.
X And Y
The Espurr's backstory in "Seeking Shelter from the Storm!". It had been cared for by an old lady, but she fell ill and died. Espurr didn't realize she had passed away, and was waiting at her mansion so that it could show her its gratitude. Fortunately, the woman's granddaughter befriends it, tells it the truth, and offers it the chance to pay its respects at the woman's grave.
The aftermath of Serena's first Showcase. She appears to take it well, congratulating Shauna on her win...but the next morning, she breaks down crying over her first-round loss. The fact that said loss was caused by a simple oversight (not cutting Fennekin's ribbon so it wouldn't trip) makes it that much more tragic.
Goodra's departure in "Beyond the Rainbow!" can't help but make you want to shed tears.
The Reveal that the antagonistic Florges was merely trying to heal its baby Floette. It turns into a My God, What Have I Done? moment when Team Rocket betray her, leaving her with no way to save her infant and knowing she helped innocents get kidnapped.
Everything from the ending of "The Tiny Caretaker". Bonnie rescued a hurt Tyrunt that had been stolen by Team Rocket. She helps clean it, feed it, play with it, and the two become close. When Tyrunt, Bonnie, Dedenne and Bunnelby get abducted by Team Rocket, Bonnie is the one who is able to defend the Pokemon through wit and guile, Tyrunt even evolving into Tyrantrum. She asks to keep it, only to find out it belongs to someone else. It breaks her little heart to see she has to give it up; and the others can only reassure her it will be better for everyone.
At the end of "Facing the Grand Design", the good Malamar pull James's Inkay, the hero of the episode, into their group to celebrate with them. James thinks he would be happier with his own kind, so he prepares to set Inkay free. Inkay pointedly tells James (via Meowth) that he wants to stay with Team Rocket, and they all start crying together. The moment takes some cues from "Pikachu's Goodbye".
After getting outright destroyed by Wulfric in their Gym Battle, Ash becomes depressed. This isn't your run-of-the-mill depression at losing a battle, however. Ash, seeing (and due to their bond, feeling) the pain Greninja endured, feels guilty and actually starts contemplating if he really can help Greninja reach its full potential, not just doubting their bond, but his abilities as a whole. Bear in mind Greninja chose Ash after rejecting dozens of other trainers, because it thought of Ash as its one true trainer. Also bear in mind that this is the guy who has lost five tournaments and still has a go-getter mentality. Ash is the kind of guy who can be down 5-1 in a Pokémon battle and retort by turning his hat and giving it his all, and yet this manages to utterly break him. The episode ends with a sullen Ash leaving into the snowfall at night, alone. The tone is actually so depressing the next episode preview doesn't even have any words (other than the episode name) or music.
At the same time, Greninja is also in the woods, upset. Contrary to what Ash thinks, it is actually frustrated at failing him, still seeing him as its true master, making his BSOD all the more tragic.
The Lumiose Conference actually ends up acknowledging something that a lot of fans take for granted when they complain about Ash losing in leagues; not every trainer who wants to enter actually gets all their badges. Before his first match, Ash gets challenged to an impromptu match by a trainer named Everett, who fell short on qualifying for the League at the very end. He's incredibly bitter about missing out on the League and then, after Ash beats him, breaks down crying about how other trainers who came up short feel the exact same frustration.
Ash pretty much has the worst day of his life after the conference's finale. Not only has he lost the League to Alain, but he ends up being Team Flare's primary target shortly afterwards. Ash expects Alain to help him, only for Team Flare to reveal that Alain has been working for them while Alain simply becomes unresponsive. Ash and Pikachu, now alone, end up getting hit by Confuse Ray and Ash asks Alain why before passing out. When he wakes up, he finds himself along with his team to be crucified on top of the Prism Tower ready to be experimented upon by Team Flare, unable to do anything other than calling for Alain's help.
"The Right Hero for the Right Job!" has a double whammy:
Bonnie desperately and tearfully singing to Squishy, trying to snap it out of Team Flare's control. And Blaziken Mask protecting her as she did.
Clembot's Heroic Sacrifice. Clemont has to have Clembot interfaced with the Prism Tower systems to shut it down, but Clembot alerts him that such a forceful shutdown will wipe its flash memory, effectively killing it. It then tells Clemont that there is no other choice to stop Team Flare, and thanks Clemont for making it. It then shows Clemont crying beside Clembot's inert body afterward.
In "Forming a More Perfect Union!", Bonnie saying goodbye to Squishy after the battle is both heartwarming and tearjerker at the same time because they both bonded very well during the whole XY&Z series.
In "A Watershed Moment", Ash and company find a robot tirelessly planting seeds for years after its creator has died. His grandson wants to shut it down but is convinced there is still a chance. After using some sensory Pokemon to find a boulder blocking to flow of water to the surface, they are suddenly attacked by Team Rocket. The robot at one point asks them to move because they are standing on seeds, and is attacked for his trouble. As it shuts down, a flashback to his creator is played. Regardless of what happens next, this particular moment is a tearjerker.
Ash releasing Greninja. Enough said.
And if that is not enough make one cry, then Rica Matsumoto's words will do it:
Rica Matsumoto: In the scene where Satoshi parts ways with Satoshi-Gekkouga I put my memories of Haro, my beloved pet dog who was by my side for twelve and a half years, and put them into my performance of Satoshis lines. Actually, the day I recorded all this was three days after Haro left me to go to Heaven and I had a lot of feelings swelling around inside me at the time. Id be happy if what Satoshi felt resonated with audience in a real way "Thank you, Gekkouga. See you again "
The Grand Finale of XYZ, full stop. Ash decides to return home before beginning a new phase in his journey, Clemont aims to continue improving his skill as an inventor, Serena decides to go to Hoenn to take part in Pokémon contests, and Bonnie hopes to one day become a Pokémon Trainer. While their separation was inevitable, seeing the group bond over the XY series makes it one of the most bittersweet finale of a Pokémon series yet. Even if what lies ahead may be uncertain, it's clear they will always cherish the time they spent together over the course of their journey. It's truly compounded by the above-mentioned Greninja watching his friend fly into the sunset overhead towards a new beginning.
Dedenne being sad about the group's split can count.
In the XYZ special "The Legend of X, Y, And Z," while Xerneas was able to return life back to Jan's homeland and, with some work on Jan's part, would probably return its former glory, Jan's beloved Aila was never revived. Jan stayed near her statue until the end of his days and the statue is still there in present day, which is discovered by Professor Sycamore and Alexa.
SM005 tells us about the backstory of Lana's Popplio. One day, Lana found it being bullied and abused by some Team Skull grunts and after rescuing it and having it treated, the poor thing was initially scared of humans and Lana herself despite rescuing it (though it quickly grows out of the fear). It's sad enough as it is but then you realize what poor Popplio has been through when it was first announced...
Lillie clearly loves Pokémon and has an encyclopedic knowledge on them, but her phobia prevents her from physically interacting with them. While its usually played for laughs, it's also shown to be pretty debilitating when it comes to joining in activities with her friends. She is shown to make progress on this though.
The death of the Stoutland that was Litten's mentor, from SM021:
It was clear from its introduction in SM007 that it was elderly, but its condition rapidly deteriorated. From its first scene, it had an Incurable Cough of Death.
Suddenly, just when Team Rocket is ambushing Ash, Litten puts Ember on them and frantically runs to Ash, meowing desperately at him. It takes Ash and Pikachu back to the underpass where they live, where they find Stoutland collapsed. Ash carries it to a Pokémon Center. Nurse Joy tells Ash that this isn't sickness or injury, and though she's cut off by the door closing, it's clear that Stoutland is simply nearing the end of its life. That can hit pretty close to home for anyone with an aging pet.
One can only wonder how Rica Matsumoto felt about this, given her own experience with a pet passing (which she mentioned she put the feelings into her performance of when Ash released Greninja.)
Although it returned to the bridge underpass, the next morning it disappeared. Litten ran around Hau'oli City looking for Stoutland. When it gets back to the underpass, he sees something familiar, but it was just a brief dust devil. Then, the legs of the couch that Stoutland laid on broke. With a nearby tree slowly losing leaves throughout the episode, the final leaf finally fell off, landing on the couch, and it began to rain.
Litten began wailing mournfully as Ash and Professor Kukui found him. With Litten on one side of the bridge, and Ash and Kukui on the other side, the scene had the feel of a funeral. Eventually, Litten laid on the couch by the leaf, not answering anybody.
RotomDex: Where's Stoutland? Professor Kukui: Don't Ask.
The dub gives Kukui an even more tragic response.
RotomDex: Professor, where's Stoutland? Professor Kukui: I'm sorry.
Even Meowth left him alone as he realized what was happening. He would watch over Litten. At one point he tried to get Litten to talk to him, but was refused.
Later, Ash and his Pokémon join Litten again, keeping watch over it in a scene similar to a wake. Eventually the clouds break, and a rainbow appears. The last leaf, which had landed on the couch Stoutland laid on, blew away. Litten saw the breaking clouds outside, and it looked like Stoutland. Litten cheered up, and challenged Pikachu to a battle before agreeing to go with Ash.
The worst part of all this is that it comes right on the heels of Ash having a lighthearted adventure with Pikachu where they rescue a Wimpod and meet Tapu Lele. The two episodes aired together as a double feature. Mood Whiplash at its finest.
During Ash's double battle with Olivia, Rockruff was gaining an adrenaline boost from its impending evolution, giving it a very aggressive, nasty disposition throughout the battle. When Ash calls for Rowlet to fly up Rockruff for a team maneuver, Rockruff doesn't recognise it and mauls it. When it sees Rowlet savaged and unconscious from the attack, Rockruff immediately returns to its senses and is horrified at what it's done. Even after Ash is understanding towards Rockruff's current nature and it manages to win the trial, it spends the rest of the episode visibly downbeat and remorseful.
The following episode it still laments over its actions before being attacked by Tapu Lele. It angrily wants to follow the legendary Pokemon, and when Ash tries to stop it, it bites him again. Triggered by this (and remembering its viciousness towards Rowlet again) it starts running away from Ash in a panic, making yelping noises that essentially sound like crying. By the time Ash finds Rockruff, it has already fought Tapu Lele, and is now unconscious from injuries and fatigue.
Relatively minor, but seeing Nebby put Lillie on the verge of tears in SM044 can be this for people who have played the games.
In SM047, Gladion reveals to Ash the reason why Lillie is afraid of touching Pokemon: She was attacked by an Ultra Beast, Nihilego. The tearjerking part is that Gladion witnessed the incident first-hand, but was too afraid to do anything to help his sister. It's implied the reason he avoids Lillie is because he feels he let her down, so he became a Pokemon trainer so that he could make up for that incident and protect her from another traumatic experience.
SM048 ends with Lillie being unable to touch any Pokémon once again. Fortunately, she gets better in the very next episode.
Ash's remorse after Gladion lambasts him over letting Nebby loose to cause Lillie's regression. While Ash has offended or bickered with many previous companions, this is one of the first true cases he realises he has caused serious harm to one of them due to not being careful around them. He is noticeably much more protective of Lillie following this.
The Flashback of little Lillie just before she became afraid of Pokemon. She is clutching a Cleffa doll and crying out for her mother, wandering about in a dark room with eerie red lights. It is clear she is scared and just wants her mom and sadly stumbled onto something she shouldn't have.
Gladion when he sees his little sister in trouble. He's running down the halls trying to find her, and then sees her getting abducted by an Ultra Beast. He clearly wants to help her, but is too terrified and all he can do is beg Faba to do something to stop the incident.
When Nihilego goes after Lillie, her mother hugs her tight while Gladion moves to shield her as well as all the Pokemon who are ready to protect Lillie. But it is Lusamine who saves them both, allowing herself to be captured to save her children.
Gladion and Lillie crying out for Lusamine. The former even attempts to go after her while all Lillie can do is scream for her mother to come back.
SM053: Lusamine is in her Mother Beast form. And while the original games suggest she may be doing this willingly, in the anime it's clear she is in a state of And I Must Scream, only occasionally mustering up the will to scream for her children.
SM079 confirms what the flavor text in Moon says — Minior who are out of their shells too long eventually die. Especially heartbreaking for Sophocles, who blocked the fact out of his memory after witnessing one die in front of him when he was younger.
SM084 reveals another side to Ash's Poipole: Something apparently happened back in its home world involving its "hive" and a Naganadel, but it isn't revealed what exactly it is. It draws tear drop symbols to express this sadness.
Ash and Poipole's goodbye in SM090. Neither wants to separate from the other, but know it has to be done.
It's revealed in SM108 that Mallow's mother died of an illness when she was young. Mallow's last words to her were telling her mom she hated her for always apologizing for being sick. Mallow has regretted that ever since, to the point she tells Lana she doesn't want to see her mom in Tapu Fini's mist. When she does see her in the mist, she apologizes for her previous words. Her mother thanks her for her support, and Mallow thanks her mom for loving her. Mallow then gets one last hug before the mist dissipates and her mother disappears.
It becomes even sadder when you look deeper into it and realize that Mallow's outburst was more than likely the uncontrolled result of the emotional weight of a dying parent on Mallow's young child mind. Imagining how she must have felt when she calmed down, realized what she had said only to find out that her mother was gone and it was too late to say sorry or tell her how she really felt will break even the most stoic of viewers. The way Mallow completely breaks down in her mother's arms is similarly heartwrenching to watch.
Lillie and Ash both also end up lost in Tapu Fini's mist at the same time as Mallow. It was established earlier in the episode that Lillie and Gladion are hoping to meet their father in the mist, but as Hapu explains to the others why their friends are missing, one can't help but think, "Wait, Ash hasn't lost anyone important to him..." Cut to Ash chasing after his desperately crying Torracat, who leads him to the spirit of Stoutland. Ash says hi for a moment until he remembers that it's still dead.
In episode 140, Bewear is in pain for the first time. Stufful is thrown off her back while fighting Guzzlord and she deliberately puts herself in front while Guzzlord starts brutalizing her.
In the Alola series finale, SM146:
Mimikyu fights Pikachu one more time, but stops when it sees its own reflection while hovering over Melemele Sea. It drops down into the water and sulks. After Ash and Pikachu pull it out of the water, it wanders away, no longer interested in the fight, with the drawn-on face of its Disguise smeared as if it were crying. Meowth eventually finds it, and finds out it had suffered a What Have I Become? moment because it was tired of hating Pikachu. Meowth cheers it up by saying it has plenty to look forward to in the future.
Professor Burnet tearing up when she and Professor Kukui are saying their goodbyes to Ash at the airport.
Ash is on the plane leaving for his home, then all of a sudden you see his Alolan friends and Pokemon bid him one last farewell, with tears in his eyes, Ash says goodbye to Alola.
Mallow being left behind in Alola as each of her friends departs on their respective journeys, with even her Shaymin flying off once Ulu presents it with some Gracidia flowers.
The premiere has two — an Adult Fear moment as the mother Kangaskhan tearfully hugs her baby after it almost died chasing after Mew, and Pichu realizing his weight was slowing her down and had to leave what he considered a surrogate family. The last one is more Bittersweet, as Pichu's love for his adopted family allows him to evolve into Pikachu, the very same one that becomes Ash's longtime partner.
In the fifth episode, Scorbunny wants to be Goh's partner, inspired by Goh's speech to expand its horizons. Goh accepts...until he remembers that promise to make Mew his partner. Scorbunny is absolutely crushed, believing that going after Goh was for nothing.
The origin of why Gengar was at the Laboratory in the first place. Long before it was a lab, it's trainer told it to wait there as it will come back for it, he never did. Gengar waited patiently, even scaring off potential house buyers, but eventually his loyalty grew into anger and sorrow, knowing that he was abandoned and betrayed. And the reason why Gengar was abandoned? Its trainer believed it brought him bad luck!
The Bittersweet Ending to JN017. Scorbunny finally masters Ember, evolves into Raboot, and helps the twerps send Team Rocket blasting off. But because of Goh's earlier refusal to help it learn its new move, their friendship has hit a snag as Raboot simply walks away instead of doing their usual fist bump. Fortunately, the next episode shows it still with Goh, so it's simply become more aloof.
At the end of JN022, Goh thinks that it's better to have Raboot stay in Hoenn after it helped cheer up some Pokémon. Ash, in a rare case of Tranquil Fury, questions if he went to Raboot and told it about this decision. This makes Goh realize that he doesn't want Raboot to leave...but by then, the doors to the train have closed and he runs across the other cars, in tears at his mistake, wanting Raboot back. Just when it looks like all hope is lost...Raboot arrives and he has an apple on him that he shares. Goh is moved into Tears of Joy as he glomps Raboot and takes a selfie with his partner.
The backstory of how Chloe met Yamper can count (in the episode JN029). Since Chloe was jealous of the attention Yamper got from her parents, she spitefully told Yamper that she wished he would go away. Yamper did just that, and Chloe went looking for it at the park because she felt so bad about what she said. Thankfully, Yamper saved Chloe from the Venonat and the two have been inseparable since.
In JN031, Poor Jinny getting mocked because her decision to use Feebas in the Water Pokémon contest, both by her schoolmates and by two older women. Fortunately, Ash and co. come to her defense, especially Chloe who gives the ladies a terrifying Death Glare. The triumphant tears kick in when Jinny's Feebas evolves into Milotic, wins the beauty contest, and Jinny's classmates apologize to her for mocking Milotic when it was a Feebas.
The episode expands on this: after Goh and his new friend, Horace , bonded over trying to find Celebi, Goh waited for Horace to arrive by a tree to try again. But on that day, Horace never showed up and he and his parents had to leave because of the storm. Goh thought that Horace abandoned him but we soon find out it wasn't the case.
Goh having Scyther and Farfetch'd cutting the tall grass has them reveal Ariados and Pineco — two Pokemon that he and Horace encountered years ago — and you can hear it in his voice when he captures them that he hates being reminded of that friend who ditched him as he keeps remembering that day. Moreover, he tells the two that he's so happy that they're always here for him, which shows how much he shrugged off friendship for capturing Pokemon as a way to fill the void and never be hurt from opening himself up to others.
Finally, Goh finds Celebi's shrine and a letter that reveals the truth: Horace never abandoned Goh, he came down with a fever and was unable to go outside during the storm. Horace heavily regretted this and upon finding Celebi's shrine one year later, wished to wind back time so he could tell Goh the truth. He then wrote a letter for Goh to find, apologizing for this and still stating that they were still friends. Which leads to the ending when Tokio returns, now with a Chikorita, and two Celebi flying off.
Remember in JN003 when Goh tells Ash that he's "one of those guys too?" Ash just reminded him of his failed friendship with Horace...
Zeno Robinson's Skyward Scream in the dub really shows how much Goh was hurt by this betrayal.
Goh: HORACE, YOU'RE A LIAR!!!!!
Ash's Heroic BSoD when he drops back down to Normal Class in the World Coronation series. Its Played for Laughs, but you cant help but feel sorry for Ash due to him losing three battles in a row.
While JN049 has a happy ending with Chloe catching her very first Pokemon, an Eevee, if one thinks about it, the fact that said Eevee is unable to evolve is both ironic and sad, considering it's called the Evolution Pokemon and has tried touching numerous evolution stones with nothing happening.
JN082: Kirara's Cleffa was turned into a star recently, and she wishes for a night sky just to find her Cleffa.
JN087: Regina's backstory is quite sad, with her Glaceon defending her from bullies, then Glaceon gets sick after using Blizzard too often.
The first movie has Meowth's clone telling Meowth that they don't have to fight. Doubles as a Heartwarming Moment.
Meowth: You're right, we do have a lot in common: the same earth, the same air, the same sky.
Meowth: Maybe if we started lookin' at what's the same instead of always lookin' at what's different... well, who knows.
Pikachu refusing to fight Mewtwo's clone!Pikachu. It just keeps taking every beating to its face, to the point that clone!Pikachu ends up crying in frustration and collapses from exhaustion into Pikachu's arms.
The song If Only Tears Could Bring You Back by Midnight Sons represents this scene in the CD.
"If Only Tears Could Bring You Back" might also sum up Mewtwo and Ai/Amber as well, from the Mewtwo's Origin short that got cut out of the English dub.
The biggest punch, though, is Misty's reaction. Ash has been harmed in many ways throughout the first season, but a Pikachu shock always revived him, and Misty and Brock just laughed and moved on. After Pikachu's attempts to revive Ash fail again and again, and the believed finality of Ash's demise hits both the characters and the audience, the mood of the scene continually drops, until all Misty can mutter is a pained, "Please, no." It's the only major human reaction we see, and the only one we really need to see. Sure, the Pokemon crying is touching to our childhoods, but looking back as adults, it's clear Misty speaks not only her voice but the voice of the audience. "Please, don't let it end like this."
Some people can't watch the prequel short on the Mewtwo Returns DVD without crying, and tears up just at the sound of "Chiisaki Mono" from the sixth movie.
The short in the first movie can also be quite hard to see, especially with young children. Watching Charizard screaming and thrashing about while trapped, and then seeing his utter despair as he realizes he can't free himself is pretty heartbreaking. Of course, the it turns into a different sort of tear jerker as all the other Pokemon work together to save him.
Mewtwo's entire life. He has to watch all of his friends die before he's even born, which is so traumatic for him that the scientists have to wipe his memory in order to keep it from killing him, too. Then, when he is given his first taste of the real world, he discovers that his entire reason for being is to have tests run on him, like a lab rat. Once he breaks out, he discovers that every other Pokémon is either in the wild or under the ownership of humans, who make the Pokémon do their bidding. He goes berserk at this point, and has to be forcibly taught that not all humans are bastards. He and the Pokémon clones that he created then go to live out their lives in a place apart from those who would harm them. But Giovanni comes and threatens to execute every last one of them unless Mewtwo submits to him, and has to be bailed out by Ash and company. The last we see of him, he and the Pokémon who depend on him are still hiding from humans, probably terrified that they will be found again. Can you really blame him for going berserk several times?
Well, maybe not quite in hiding. Mewtwo is alone the last we see of him, and one of his inner struggles in Mewtwo Returns was deciding to protect his clones, or let them go. In the end, he releases them to live new lives, whether in the wild or with a trainer. The last shot in the special of him gazing at the moon overlooking a human city is a powerful testament of how far along he's gotten in becoming more accepting of the world, and who he is. It also counts (possibly) as an Earn Your Happy Ending or Bittersweet Ending if you read more into the context.
Speaking of Pokémon, the capture of Pikachu by Mewtwo's evil Poké Balls in the first movie. It's been established that Pikachu does not like being in a Poké Ball. Many times. Ash is beaten half to death by evil Poké Balls and robotic arms in a chase all over Mewtwo's fortress. He does all he can do to save his buddy, and in the end, he fails. Pikachu has been captured by the Big Bad, his freedom stripped away. He gets rescued, but still...
Related to Pikachu's Poké Ball phobia, Ash demanding Pikachu get into one in "Snow Way Out" so he won't die from the blizzard they're stuck in. As if to prove Pikachu's point that he won't leave his trainer's side, his other teammates come out of their Poké Balls and hug Ash...
Also from that episode, the flashback to Jessie's childhood. She was so painfully poor that a meal entirely made of snow was a delicious meal to her.
During the second movie, Team Rocket's attempt at Heroic Sacrifice when they let go of Lugia so as not to slow him and Ash down. Their "last lines" are just too priceless: "Let's not say goodbye/Let's just say/We're gonna die." Of course, they live, but still...
Don't forget their variation on their usual send off as they fall: "Team Rocket's blasting off for gooooood...!"
And then, not long after that, when Lugia is zapped by Lawrence, it falls into the sea with Ash and Pikachu. Pikachu and Ash surface, and Ash is unconscious. Misty and Tracey fish them out of the sea, and Misty has to give Ash CPR.
The scene in the 8th movie where Lucario sacrifices himself to save the Tree of Beginning.
Also, during the aforementioned scene when Lucario discovers that Aaron only trapped Lucario so that he wouldn't follow him and suffer the same fate. And during the ending credits, Lucario and Aaron eating the bar of chocolate Max gave Lucario earlier in the movie.
Celebi's "death" in the fourth movie. Ash and Sam's reactions were bad enough, but seeing Celebi's shriveled, lifeless body pushed it over.
Also from Movie 8, Ash calls out all of his Pokémon as he's being absorbed by the energy orb-gunk and, in the dub at least, he says goodbye to Pikachu and tells him he loves it as he gets fully absorbed. The sight of Pikachu and all of Ash's Pokémon at the time crying, including Grovyle(!) was like "Mewtwo Strikes Back" all over again. Then when Ash, and everyone else comes back, Pikachu, with tears in its eyes, hugs Ash. Then Ash gets glomped by Phanpy and Corphish while Grovyle and Swellow watch.
Ash: Pikachu, you can't save me! Just take care of yourself, and all the others! I'll miss you, buddy, I LOVEY-!
And just the way he says it all as fast as he possibly can while still being coherent. Just knowing that you have about ten seconds to say everything you need to, to say good-bye...
Latios' final goodbye to Latias, in the fifth movie. The way the now-translucent Latios takes Latias' hand, and then Latias realizes, confirmed with Latios simply nodding, before the two's grip breaks, and Latias is pushed away, this heartbroken look on her face......... It's really not helped by the scene a few minutes on, which shows the Earth/world e.g. what Latios is seeing, through his psychic connection with Latias, for the final time.
Especially since the creator of Pokémon always used the word "faint" to describe defeated Pokémon so that kids wouldn't have to hear about death. This makes the first on screen Pokémon death even more moving considering that Latios sacrificed himself to save his little sister Latias, and the town they lived in and explains in the games why Latias learns Wish and Latios learns Memento.
The end credits to the third movie, partially because of the song playing ("To Know The Unknown"), and partially because of one scene that shows the return of Molly's long-lost mother.
Also from the third movie, the part when Ash is falling into the pit, and suddenly Charizard, the Pokémon that previously hated him and refused to ever do what he said, swoops out of nowhere and saves him.
Molly's parents both disappearing, one leaving her family, the other being dragged into another reality. Also, the whole part about rejecting her reality in favor of living in her dreams. The entire OST of the movie emphasizes the isolation and loneliness Molly experiences.
During the very vicious tussle between Entei and Charizard, Molly begins doubting her actions. However, it is right when Entei is about to deal the killing blow to Charizard that she breaks down in tears, begging him to stop and return everything to normal. This itself has sad conclusions since it means all the friends she imagined, including Entei itself, must disappear from existence.
In the 10th movie when Darkrai couldn't block Dialga and Palkia's attacks anymore and they strike him, which ends up killing him. Thankfully, Palkia is able to restore him along with everything else at the end.
Darkrai's (and no doubt by extension all Darkrais') backstory. Being reviled by everyone just because you have a power you can't control...
Considering what he does is basically an uncontrollable self-defense mechanism... it is. Well, except that one Darkrai who almost succeeded at plunging world into eternal darkness. He gets better after his memory is accidentally wiped out, though.
The ninth movie had a lot. First, May realized she had to part ways with Manaphy which makes it even sadder because Manaphy thinks of May as its mother. Then, the ending where they had to part ways. Manaphy says May's name which it learned all on its own. As May tearfully says good-bye to Manaphy, its last words were "Bye, Love you May" (In the Japanese version it was 'Sayonara, Haruka'.)
"Chiisaki Mono" (the ending theme for the 6th movie) Same for "One" (the ending for the 11th movie). "Soko ni Sora ga Aru Kara" has the same effect.
The scene in the twelfth movie where Arceus saved Michina from the meteor. You know it gets better, but seeing it lying there in the snow, with all of the other Pokémon cuddling up to it and trying to keep it warm... And then, when Damos uses his special ability to see the hearts of Pokémon, Arceus is just grey... like the rocks it's lying on...
It is worse when you remember what Arceus is. A creature akin to a god is dying. A god. Is. Dying.
And on top of that everyone from the future is fading - because they might not even exist if Arceus dies here! Ash is the last to go, and he just manages to get the Jewel of Life to Arceus before disappearing completely. Thank goodness the process is reversed with Arceus' survival.
Before that, the Big Badstarts his (modified) plan to kill off Arceus in the past, using its weaknesses to Lightning, Water, and now Metal. Seeing Arceus, at this point compassionate to humans, being ravaged by the attacks and slowly drowned in molten silver is a gut-wrenching thing to experience... and is no doubt intended to be seen as such.
The look on Ash's face when he finally brings the jewel to Arceus and fully realizes the state it's in. The poor thing looks like it's already dead, with nothing but a faint glow of red left in its eyes.
Lawrence in the end of the second movie. Sure he was greedy, but he never came across as evil, and to see him wandering aimlessly in the ruins of his collection only to find the one scrap left. He picks it up and stares blankly over the ocean. To add onto it, that collection of his was made of ancient artifacts. That's world history that just got vaporized.
The scene in Pokémon: Zoroark: Master of Illusions where Zoroark dies after risking everything to save and protect her baby boy, Zorua. To elaborate, Zorua has gone through an endless amount of pure crap and has gotten shocked to the bone, kicked around, and almost killed by the villain, and Zoroark has done everything in her power to protect him (and trust us, she is VERY powerful). And then she just can't take it anymore and falls to the ground, dead as a doornail. Thankfully, she gets better.
Made worse when Zorua spends the next few minutes trying desperately to wake her and finally bursts into tears. He then makes an illusion of their home, begging his mother to wake up so they can finally go home and be together again, finally ending by screaming his pet name for her at the top of his lungs, heartbroken. And even more, Ash's voice actually cracks with grief when he tries to wake her as well.
To add punch in a guts: in the Russian dub Zorua calls Zoroark "Bulya" which is short from "babulya", Russian for "grandma". So, if she's his granny and he lives with her... then what happened to his parents? Given how desperate Zorua was to wake her up, it could only mean that his parents are dead...
Pokémon the Movie: Black/White — after trying so hard to get Victini free, those pillars clouded around him, and all seems hopeless, a shivering Ash apologizes for not being able to keep his promise, sheds a tear that freezes in midair, and seemingly dies. Victini then pulls off a Heroic Sacrifice that wakes Ash up, making it a Disney Death at the end of the movie.
In the XY-era film Diancie and the Cocoon of Destruction, it's Pikachu's turn to die. He had been barely clipped by Yveltal's Oblivion Wing attack, and ended up turning to stone in Ash's arms. After a brief moment of grieving, Xerneas emerges and engages a Heroic Sacrifice to restore Pikachu and everyone else afflicted by Oblivion Wing (including Team Rocket), as well as restoring an entire forest, at the personal cost of turning into a tree.
An early novelization by one of the anime's major writers talks about Ash's father. They fell in love, married at age eighteen, and he ran off onto his journey. To top it all off her mother had just died and Delia was left with a restaurant and a newborn. He's been missing ever since and has achieved little to nothing. Ash's mother has exaggerated his father's legacy, not wanting to ruin Ash's perception of him. He was a mediocre trainer.
The same books say that being a gym leader is a terrible career. They are disqualified when they lose three times in a row, so they often bribe challengers to let them win. It costs a lot of money and the government doesn't give them enough. Brock's siblings have many fathers. They kept on running away and so Brock's mother had to marry again and again, having multiple kids. Eventually she ran away herself. Brock is so love-struck because he wants a woman to help take care of his family. The book states Misty's parents ran away but it doesn't give much info about them.
Note that these books are most likely no longer canon, as these details contradict many things in the anime proper.
Takeshi Shudo's novelizations depict the world of the anime as a Crapsack World, with Gym Leaders being fired if they lose three matches, 10-year-olds being legal adults and having to pay taxes, go to jail, or marry, and many, many fathers and grandfathers leaving their families only to get nowhere on their Pokémon journey.
Shudo apparently wanted Pokémon to end with a revolt or rebellion of the Pokémon, who made Pikachu their leader and Meowth some ambassador or translator, and Ash would realize his dream of becoming a Pokemon Master was a childish dream that he needed to wake up from.
"Pika Pika Massaichu", the Japanese ending theme to the first Pikachu short, can make one feel very nostalgic for summer vacation and childhood, especially when you read the translated lyrics.
"Meowth's Song"; an image song used in the Japanese original. While it is briefly used in the dub with completely reinterpreted lyrics about trying to impress Meowzie (which itself is rather tragic), the original full song has Meowth lamenting over his constant loneliness as he philosophizes under the moon. Here it is with translated lyrics.