Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
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 Vetrix (the only one in the series aside from a few flashback losses to Quinton). His hunt is over, and everything he's done has been for nothing. And then, as Vetrix tries to attack him even after his life points are gone, Haruto protects his brother, before Kite is lowered to the ground to the tune of music that always evokes an emotional response, and his soul is taken. It made this troper shed tears for the first time in the series.
Somewhat surprisingly, Vetrix's falling into the Sphere Field come's across as this. It's Yuma's reaction that really drives it home.
A strange one in the final duel against Faker after the Barian possessed him. When Haruto uses his powers to defy the Barian 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 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 disappearance. She also bids farewell with Nasch by using their real names.
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.
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.
It should also be noted that it appears that Nasch's death, Kaito's death and the deaths of the Barian Emperors were final. Essentially, Yuma will return to Earth after in all likelihood killing Astral going by the tendencies of the latest duels to see that his closest friends are dead, and never came back with the other secondary characters. The Door's Prophecy Fulfilled.