This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Wonderful 101
From Earth Defense War II: Arthur Wedgewood, Wonder Red's father, sacrificing himself to save his son and the entire Earth. The scene is only made even more heart-wrenching by Young Will's expression and the final line of the flashback:
Young Will: (reaching for Arthur, teary-eyed, while being carried away by Nelson) No, let GO! Let GO of me! Dad! DAD!!
Vorkken and Immorta's backstory certainly counts: Vorkken was once a kind prince on Rhullo (and Immorta was likely a princess as well, being Vorkken's sister), but when the GEATHJERK attacked, all his subjects, his entire family aside from Immorta, and the love of his life were murdered, and Rhullo was completely destroyed, leaving Vorkken and Immorta as the last of their kind. While Immorta joined the Galactic Federation to go after the GEATHJERK, Vorkken became obsessed with gaining power to take revenge, finding and defeating the strongest warriors from various astral bodies to amass an army. Eventually, he lost track of his mission and became obsessed with power for power's sake, resorting to allying himself with the same force that destroyed his home (though to be fair, he was also somewhat brainwashed by them) for the sole purpose of becoming stronger, leading to him becoming a space pirate with almost no shades of his former self remaining. Wow.
Luka and Platinum Robo AKA Professor Margarita AKA Luka's mother's reunion. When the team enters Platinum Robo, White sums it up as such:
Wonder-White: It feels like melting into a mother's warm embrace...
In a bizarre villanous example, Jergingha's lines regarding the future the GEATHJERK came from wherein they were conquered and brutally oppressed by the evil Wonderful 100 and the Greater Galactic Coalition are actually rather sad.
Jergingha: Now I finish my task and end our nightmare forever!
Most of the Wonderful Ones' profiles are lighthearted, even goofy. Wonder Bonsai's is not. He's an old widower who feels he has nothing left to live for after his wife's death, and seeks to die on the battlefield.