Blue receiving the Pokedex in the penultimate chapter.
Red getting the living crap beaten out of him while Pika could do nothing but watch and cry "Piiiiiiiiii!" was incredibly heart-wrenching.
We see a peek of Lance's past, and as a little kid, he sees a bunch of Pokemon dying in industrial waste. As he desperately hugs a Dratini to his chest, crying, his Viridian powers let him feel just how much it's suffering. The experience was so bad that even after his defeat, he didn't perform a Heel-Face Turn, not exactly. He still held the same views that Humans Are Bastards; he just knows that he'll fail if he tries to Kill All Humans again because Yellow will stop him.
It's brief, but it's kind of moving that Lt. Surge is visibly horrified at the notion that the Masked Man drowned two boys. It really feels good after the Yellow Arc had just about everyone hoping the Team Rocket members had some permanent Character Development.
Likewise his horror and pleading with his men to recognize him when the Mask of Ice is controlling them. After freeing 3 of them he tells them to help the others while they beg him not to go.
Crystal's distress after getting her butt kicked by Suicune and losing her capturing skills. It's really sad to see Crystal so broken and upset, and even more so if you've been in a similar situation where a traumatic event makes you lose the ability to perform your special talents, especially if you lose them forever, depending on how severe the trauma and injury is. It doesn't last long though, and she gets better.
Janine's reaction, after forfeiting her match to Falkner to pursue the man she thought was her father, only to realize that it wasn't Koga, made this troper seriously wibble. Her words to Falkner, after he catches up to her, don't help at all.
Janine: You mentioned that you'd follow your father's footsteps and become a leader. It seems that I have fought a similar opponent again... I guess this is my fate.
The "Fatherlyshipping" fandom this scene alone inspired has such a following it actually reached to the Pokemon Company, as Heart Gold and Soul Silver hint that they are now an official couple.
Janine is also just so damn nice, compared to her father, that one can't help feel sorry for her for the inevitable moment she actually finds him and learns of his sinister deeds.
There have been hints of it throughout the past two arcs, but Blue's past is finally revealed in its fullness...good lord this girl went through shit, yet she remained determined the whole time to bring an end to the one responsible for her pain and protect the ones she cared for.
Silver's Heroic Resolve to protect Blue, the one person in the world he cares about, is touching. When he gets the tar beaten out of him by Will and Karen, it's heart wrenching. Then we find out he couldn't bring himself to fight them properly because he was afraid they were working with the Mask of Ice because they had Stockholm Syndrome which makes it all the worse when Will laughs in his face
The end of the Gold/Silver/Crystal chapter of Special, when we find out Pryce's reasons for wanting to be able to travel through time, and we hear the song, "A Boy and his Lapras". Not a total villain, after all; just really misguided.
This Troper lost it when we see Gold, eyes closed, seemingly lost in time. He isn't. It's still sad, however.
Red is trying to come to terms with being unable to become the Viridian gym leader due to his injuries from his fight with Lorelei. While he is told of a cure soon after, he tries hard to accept that he will never be as strong as he used to be and must ask Green to carry his responsibility.
Starting with their meeting at Fortree City, just about all of the scenes Ruby and Sapphire share with each other are this.
The incident at Fortree City is particularly jarring because of how it starts so pleasantly, with the two beginning to find common ground, get along, and reveal they have hidden depths to their rather extreme personalities. Then, Ruby enters his Moral Event Horizon, and Sapphire lets loose a "Reason You Suck" Speech so severe it actually moves her to tears.
Most notably, the flashback both have simultaneously, to the moment they were children and good friends, plus the traumatic event that changed their lives forever. Neither realizes the friend they met then and dedicated their whole life to is their current rival/temporary ally, but of course we do—and it is beautiful. The really sad part? Wondering if they will live to learn the truth about each other.
Ruby was so horrified by this event (specifically how scared of him Sapphire was and the trouble Norman got into) that he vowed never to battle again. Norman and Sapphire have given him a fair amount of flack for his unwillingness to battle not realizing his reasons
Then, They do learn, in the process of confessing their feelings for one another. The sad part here? Ruby just leaves Sapphire locked up to protect her from the battle, which also implies he believes he may very well die, and Sapphire undoubtedly believes it, too. Of course he doesn't, but he comes close.
After the action finale, the ending scene is mostly for laughs. Yet it's still kind of sad we never got to see them kiss. Oh well; at least they're friends now.
Toward the end of the arc...
Ruby: Because of me, you sacrificed your dream, your honor... everything!
Also, when Mimi came back to Ruby, after everything he'd done. Ruby's speech, along with the fact that he's crying too...*sniff*.
A minor detail that speaks volumes if you think about it. With Wallace is getting the crap beaten out of him, Norman's corpse is being burned, Winona is unconscious from being strangled, and Ruby barely staying conscious in her arms, Sapphire looks ready to break down. People important to her are getting hurt and she can't do anything about it, just like how it was during the Salamance incident.
Blue and her parents. Just Blue and her parents. The first time she sees them in twelve years, they're sucked into a big black hole (No wonder she went near-comatose afterward). Then when she finally gets to talk to them, she has to leave them behind because, as she says through her own tears, "it's her destiny to fight evil." Godspeed, Blue. Godspeed.
The near end of the arc when Giovanni saves Silver from flames. Silver still rejected him after that, but was given a talk by Green. Then he cried.
This troper has seen people who've cried over this scene.
Likewise just when it looks like Blue might be able to have an actual conversation with her parents and that Silver can come to terms with his heritage they are attacked by Sird who turns the heroes to stone and Oak tries to keep Blue's parents from seeing what has happened to her.
Emerald's back story.
The ending. Giovanni is able to get his medicine and helps save the world... and then reveals that he was Evil All Along and leaves Silver behind to rebuild Team Rocket. Gold and Silver turn down his offer to join them, and Silver is shaken by the entire experience, vowing to make his dad turn good.
Diamond and Pearl arc- when all three protagonists wake up the first morning after separating to defend each of the lakes, each of them is reflecting on the morning routine they shared with each other for the last month, only to realize that now they suddenly feel very alone without the other two. All three of them start crying, and it's just a heartbreaking moment.
Made all the worse because Diamond's catchphrase of "I'm Pokeaayy!" after getting hurt is the result of Pearl telling him he needed to think up a good one line gag. Pearl is crying over his friend begging him to say that line.
N reveals to White that Gigi has always wanted to battle instead of just performing. When White tries to jump out of the Ferris Wheel and urges Gigi to do the same...Gigi abandons her, deciding to stay with N. White slips and falls, and she's left as a sobbing, broken wreck on the ground. Jesus, how many plots do you have of a Pokemon abandoning its trainer and the trainer being heartbroken as a result?
A lot, apparently, seeing that they decide to reveal that Black's dreams have changed and aren't appealing to Musha anymore, who decides to bail on him.
As it turns out, N was wrong about Musha leaving; it decided to leave to get stronger, in hopes that Black's dreams would return if it did.
Black ends up trapped in the Light Stone. White tries to pick the stone up, but it flies away before she can even touch it. She breaks down and cries as the stone flies out of sight.
Even worse? He reveals to White before disappearing that he never forgot about his promise of advertising the BW Agency in the Pokemon League. His last thoughts are of whether he managed to pay off his debt, which White shakily admits after he's gone that he already has.
We get a major one right off the bat: X used to be a promising, up-and-coming trainer, but now is a depressed shut-in who refuses to leave his room no matter how much his friend pleads with him to come out. Everything points to the paparazzi being at fault, and you wonder just how bad things went for him to go down this far.
Also, unlike her game counterpart, Shauna is much more pessimistic, likely stemming from watching all of the above. And yet, despite doubting things will ever change, she still hopes for the day all of her friends can be together and happy again. Finally, she ends up losing one of her Pokemon when her hometown is destroyed.
The series opens with the heroes' hometown being destroyed.