Gash Bell has several such scenes, notably Gem's final words to Yopopo in episode 22 and Kid saying good-bye to Professor Riddle before going out in a blaze of glory in episode 73.
Oddly enough, it was Byonko that did it for this troper. Particularly, Demoruto burning Byonko's toy clock, and the implication that Alvin would be all alone again.
Patty's departure as well, especially when, as she's disappearing, she tearfully tells Gash and the others that regardless if they forgive her or not, to please be friends with Byonko when they all return to the Mamodo World, since he was always so lonely. It really cements how Patty has completely grown past her selfish ways and become a truly good person. It's a heartwarming moment too, as Gash responds that they'll be friends with Byonko AND Patty when they return to the Mamodo World, as Patty is a friend too.
There are two other moments that always hit this troper: Danny's goodbye to Mr. Gold, in volume 7/episode 27, and Albert bringing Leila back from the stone illusion, in volume 16/episode 78.
Kiyomaro's apparent death at the hands of Leo. Full stop.
His final thoughts being a wish for Gash to find a good partner who will help him become king. This series runs on tearjerking and heartwarming.
One name. Kolulu. Damn.
Poor Won Lei and Lee yen's relationship seem to be chock full of such moments.To begin with, there's the little fact that they would have to split up sooner or later when Won Lei returns to his own world. And then there's the fact that Lee Yen's Mob leader of a father did everything he could to break them up, at first. And then there are the multiple occasions when Won Lei fights to the last ounce of his strength and then some,to protect Lee and her friends from unstoppable opponents in one man stands that are nearly as epic as they are heartbreaking. Of special note, is his final battle against Unko Tintin,where they fight together even though they can't even communicate via any way except for their innate understanding. In the end, Won Lei shields Lee, Megumi and Tio from Unko Tintin's strongest attack even though his book is already burning and he is running on a completely empty tank.
The burning of Nya's book in an anime filler arc. Sadder in the original than in the English dub, which had more dialogue that bordered on melodrama. In the original, most of the dialogue consists of Shion repeating her friends name, on the verge of a Heroic BSOD.
What immediately follows is also one. Gash and Kiyomaro cry out "how could you do that, You Monster!!?" to the villains who burned Nya's book. The Mad Scientist finds this reaction uncalled for since burning books is a rule of battle and even Kiyomaro and Gash themselves have burned opponents' books in the battle to become king. To which Gash tearfully replies that's not what he meant: their anger is over the fact that Shion and Nya trusted these guys in helping to keep them together, but knowing exactly how much Nya meant to Shion, the bastards lied to her and Nya, toyed with their feelings, and then ended up making what Shion had been trying to prevent from happening happen! They deliberately made a false claim AND did the exact opposite of what they claimed they would do. And to Kiyomaro and Gash, This Is Unforgivable!.
The end of the Zophise arc, seriously. First, there's Sherry and Koko's reunion with the latter thanking the former from the bottom of her heart. When Sherry leaves the room, even her butler is bawling like a baby. And, as if that moment alone wasn't enough to make us cry, we have Sherry, in tears, pledging her loyalty to Brago, swearing to make him the king while we see shots of how he developed through the story and become someone who genuinely cares about Sherry and other people, not just himself and his desire to be king. I mean, seriously. Even thinking about it makes my throat go dry....
Speaking of Koko, there's all of episode 85. Koko gives Sherry a drawn-out, cruel Mind Rape by revealing the Broken Pedestal Sherry has put her on; that she is NOT mind-controlled by Zophise and has actually always been a cruel person who hates and resents Sherry and even stole from her when they were kids. Sherry loses the will to fight, and Brago fights on anyway, getting absolutely trashed by Zophise, and Sherry can only watch helplessly while breaking down crying. And then Sherry notices the sun and moon rings she's wearing, that Koko made for her when they were kids. She realizes that Koko is still wearing the matching sun and moon earrings, and that Koko, in the midst of her sadistic taunting, had been subtly telling Sherry to notice this. As clear as day, Sherry realizes that it all has been a trick of Zophise's all along, and that the real Koko who is her friend is still buried beneath the mind-controlled personality, begging to be saved. Sherry finally regains her Heroic Resolve and helps Brago recover, the two of them going on to defeat Zophise and save Koko.
Folgore's past is also one. He was a dreaded delinquent, who beat up anyone in his way. This was to the point where his hometown feared him and was often alone. He was eventually kicked out of his parents at gunpoint. His total change from that to the Italian idol was a way to atone for that. Despite how much he genuinely changed and all the good he does, his parents still won't talk to him.
While carrying Gash and Kiyomaro to the final battle, Ponygon looks back at his memories in the demon world: his parents explaining to him the meaning of their clan’s pride; he and Gash saving his father from dying of poison; and his mother telling him how he can find happiness in life. In that moment, just before his book is burned, the entire meaning of his character is established to that of a loyal and best friend to Gash, just like he was since the beginning.
Towards the end of the manga Papipurio, one of the closest characters you'll find to a scrappy in the series, gets a surprisingly touching moment when his partner nearly sacrifices her life to ensure his safety, acknowledging that she always treated him like her own son who had died years ago. They get a temporary reprieve, but end up getting bumped off shortly afterwards along with one of the manga's major characters. (Which is one hell of a Tear Jerker on it's own)
This troper was starting to tear up when Danny and Gash's other friends showed up to help him against Clear Note, and completely burst into tears when Koruru showed up.
The second to last chapter. After finally winning the kings battle Gash and Kiyomaro have to say goodbye forever. It gets worse when you realize that they knew this was coming for months and they still can't keep straight faces. Just to round it off in the background there's Sherry bawling her eyes out after she's lost Brago too. It was the most emotional thing this troper has ever read in his life.
The last attack of the fight as well is a massive one for the rivals. Gash and Brago fire off their ultimate attacks, and Bao Zakeruga wins the clash. Sherry's desperate to the point of hysterics over her inability to keep her promise to make Brago king, and then... he reaches out, grasps her hand, and makes her drop the book, saying that he would never have made it this far without her and that he was proud to have her for a partner. Then the book is incinerated. That is how you make an entire series' worth of character development pay off.
This troper has cried plenty of times at anime, but never at a manga. When he saw Kiyomaro begin to cry at his graduation ceremony he began to sob. Hard.
Gash's past is just depressing. He was sent off to live with a horrible old woman, who at least started abusing him when he was THREE. He had little friends and was made fun of a lot for being weak, the old woman would beat him and force him to do all of the chores, which included cooking and cleaning. She outright lied to him by telling him he had no parents. He pretty much went catatonic until he heard he had a real family, and he became a Stepford Smiler. Then he finally meets his twin brother, who then erases his memory.
Episode 108, full stop. Gash's desire for a mother is so pure and heartfelt, and the ending...
Ted, despite being already fighting a really powerful rival, keeps receiving the attacks of Cherish, claiming they don't hurt and still smiling at her, which makes her realize how brave he is and how much she touched his heart. This is enough for her to stop fearing Zeno's electric powers and fight back.
The first five episodes alone have enough crying to drown a whale and hide the city of Atlantis.