This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Yu-Gi-Oh! ZEXAL
While mostly everything about Tron is generally Nightmare Fuel, the way he cruelly berates and insults first IV, then his brothers too in Episode 59 is really heartbreaking. IV has done horrible things and become pretty messed up all in the hope of turning Tron back to the loving father he used to be... and Tron himself crushes his hopes and calls him and his brothers a failure. It's... heartbreaking.
Kaito's defeat at the hands of Tron (the only one in the series aside from a few flashback losses to V). His hunt is over, and everything he's done has been for nothing. And then, as Tron tries to attack him even after his life points are gone, Haruto protects his brother, before Kaito is lowered to the ground to the tune of music that always evokes an emotional response, and his soul is taken.
Somewhat surprisingly, Tron's falling into the Sphere Field comes across as this. It's Yuma's reaction that really drives it home.
A strange one in the final duel against Faker after Vector possessed him. When Haruto uses his powers to defy Vector and reunite Yuma and Astral, the music played during the scene makes it a very emotional moment.
In episode 111, Astral dies. The outro of the episode is even changed into a Clip Show showing moments of interaction between Yuma and Astral along the series to reflect this.
In episode 120, Shark is finally confirmed to be an incarnation of the former Barian leader, Nasch. His response to this is breaking down in tears and stating that it is a cruel fate that he is actually the very enemy of those he has learned to think of as friends and companions (namely Yuma, Astral and Kaito). The music doesn't help.
Episode 125: After the Barians make a comeback with their ace monster, one by one those who were facing them die. All of them upset they were unable to help Yuma. It is this moment that IV, who up to this point was trying to reforge Nasch's bonds with his friends gives up and simply wants to take him DOWN.
Episode 126: Cathy pushing Kotori to go with Yuma into Barian World instead of her. She pretends that she does it because if she went, Yuma wouldn't stop thinking about her, but the truth is that she knows Kotori is the one Yuma loves, and she's barely holding back tears on account of this heartbreak.
Episode 128: The clip show starring III, IV and V at the credits
Episode 133: After Durbe is defeated by Vector in the previous episode, Merag and Girag are defeated by him as well.
As for the case of Merag, upon her defeat, her memories with her brother is also shown before her passing. She also tells him to be strong and live on, he is not alone, and eventually bids farewell with Nasch by using their real names. She also wishes to be with her brother for a bit longer upon passing.
The outro of the episode is even changed into a Clip Show showing the good times and past lives of Girag, Alito, Merag and Durbe to reflect this.
Episode 135: The death of Kaito. And unlike the Barians, who it could be argued have simply been reduced to souls, he dies after WINNING, and his spacesuit (Orbital 7) gives out. Cue the obligatory Clip Show...
Kaito's death is especially sad. Not because he's one of the Power Trio, but because, up to this point, characters that have died are transferred to Barian World as energy. Kaito doesn't, dying on the moon due to likely a lack of oxygen.
The dub unintentionally makes this worse. In order to pull a Never Say "Die" moment, Faker tells Kite that medics are on his way. However, Kite's spirit appears while Yuma and Shark/Nasch are dueling Don Thousand implying that he didn't survive.
You can't help but feel sorry for Vector, of all people, after seeing his true memories.
Episode 143: Shark/Nasch's death following his duel with Yuma.
Episode 144: Astral has finally obtained all 100 Numbers, and tells Yuma that he is going to fulfill his mission and use the Numeron Code to destroy the Barian World. Yuma is incredulous, and starts questioning why Astral would do this, eventually challenging him to a duel to determine how the Numeron Code will be used. Astral agrees to the duel and adds that he will erase Yuma's memories of him should Yuma lose. When Yuma is preparing his deck later, he wonders if he and Astral didn't understand each other as well as he thought they did after all.
Episodes 46-49. III's absolutely breaking/broken from how much his family has changed.
Episodes 57-58. Pretty much the above, except applying to IV now. And to add to this, Tron brutally does not give a shit about IV's feelings, even helping his opponent, Shark win.
Episode 67: After acting absolutely inhumane for half of the series, Tron willingly lets himself get sucked into the Sphere Field, giving back all the souls that he took in the process...including the souls of his sons, finally showing that he does care about them in the end.
Episode 111: Astral dies trying to defend Yuma from Number 96's attack, taking the blow himself, and having to withstand the corruption. Yuma and Kotori are utterly in tears, and Shark and Kaito are also saddened terribly.
Pretty much the entirety of Arc 6 (Episode 124 and on). Most of the supporting cast dies, along with the Arclight brothers. Shark and Rio, having now become Nasch and Merag, are trying to play themselves as cold and ruthless, but cannot do so. Don Thousand's meddling with the lives of Alito and presumably the other Barian Emperors is revealed, and Vector tries to take the rest of the Emperors out. And, of course, Durbe dies.