In SEED Episode 40, during the Heroic Sacrifice of Uzumi Athha, who tells his little girl Cagalli that although she was adopted, he was so glad to have been her father before spiriting her off to freedom, Fiction Junction's Chariot of Dawn acting as a heartbreaking funeral march did not help to stop the tears from pouring down. Damn you Yuuka for your beautiful singing voice!!
Kira's response: "Maybe this was all a mistake." His girlfriend is breaking down in front of him, and he's too emotionally drained to deal with it. Highlights how badly both their lives suck. Made even worse when Kira refuses to see his parents, noting that, "all they'd see is a soldier" and that he'd have to ask "why the hell they made me a Coordinator."
"This is what I do: I pilot a mobile suit, and when I'm not fighting, I help other people build mobile suits. Why? Because I can."
Perhaps one of the biggest reasons for why Flay's death was more tragic than she deserved was not just because she truly regretted her actions and behavior in the series, but because, in the end, she was never able to properly make amends with Kira or Sai, or anyone else, which is what she desperately wanted to do now. And, if that weren't enough, according to Word of God, Flay's spirit never actually appeared to Kira, meaning while we got to hear what Flay wanted to tell Kira, he never did. It's somewhat better, however, knowing that Kira still forgave and loved her regardless of her never being able to make things up to him. He's just that kind of guy.
Nicol's death. Made worse when you realize that the episodes leading up to it foreshadowed it to high heaven.
Followed by Tolle's death. My God, poor Miriallia... *sob*
And the scene that follows that: Kira and Athrun beat each other down in what is probably one of the most brutal Gundam fights ever animated. All while sad music is playing. Here are two best friends, who still care for each other after all these years... and they're trying as hard as they can to kill one another, both out of rage at the loss of their comrades, and out of a feeling of sheer futility in trying to deny that they are enemies now.
There is a short scene in one of the last episodes, showing the insight of a hangar full of damaged Strike Daggers and an Earth Alliance pilot holding another one in his arms, appearing to look for a medic, we then see the face of the carried pilots who has blank eyes, either an indication of being dead or in coma.
Find the Way, the final ED for the series, is most certainly Tear Jerking Music. Both the song itself and the imagery of the credits screen really tugs at you.
Another small moment is the sinking of Vesalius, with Captain Atus saluting Athrun, Dearka, and Yzak as fire engulfs the bridge.
Early in the show there is the Mutual Kill of EA Admiral Lewis Hallberton and ZAFT Captain Zellman, with each man sacrificing himself for the future of his side. Ramius and Nicol's near simultaneous Say My Name moments ("Admiral Hallberton!" "Captain Zellman!") drive it home.
When Shinn unknowingly killed Captain Todaka, the man who rescued him after his (Shinn) family's tragic death. The fact that they showed how he rescued Shinn in a flashback after his death really made This Troper feel depressed... =(
This troper finds the moment just beforehand even worse. Shinn actually succeeds in Defusing The Tykebomb, and Stellar has a momentary fantasy of being reunited with him, and she looks so happy. Knowing what's coming makes that moment absolutely devastating.
Another of the few truly touching moments in Destiny was Meer dying after Taking the Bullet meant for her idol, Lacus Clyne, and Lacus crying after she reads Meer's digital diary and learns about her backstory.. The Famous Last Words spoken there are among the saddest in the whole franchise: "Lady Lacus... My life, my song... please don't forget them... I'm so sorry!"
And then we have her funeral, where she's mourned by everyone in Lacus's crew and her body's shot into space in a capsule.
Lacus: " Miss Meer, I will never forget you"
It's only a Clip Show, but Episode 29 of Seed Destiny, "Fate" always leaves me feeling like I've just been kicked in the gut. Durandal and Le Creuset's ghost arguing over the human experience while we flashback over every, single one of Seed's most depressing deaths is bad enough, but it's only made worse because Le Creuset is narrating for most of it, and we're treated to the flashbacks from the end of Durandal and Captain Gladys' relationship. The episode is absolutely emotionally draining to watch, as it shows you just how far gone Le Creuset was, and actually leaves you rooting for the Chairman, while giving you a lot of insight into how he got to be that way. The incredibly sad music does not help, nor does Durandal's obvious depression. Probably one of my favourite, if saddest, Gundam episodes, and the one that got me hooked on Destiny.
The final confrontation. Rey is moved by Kira's ideals that every individual can improve and betrays Durandal who has been following since an early age. Although Durandal is still happy since Thalia is besides him, Rey breaks out crying. As the ship where the three is falls and Thalia hugs Rey who in his last moment calls Thalia "mother."
Shinn went through a sad fate during the final fight against the Archangel but it did not get as bad as Rey's. After losing his mind fighting Athrun, Shinn is defeated and wakes up besides Lunamaria. The two embrance sad when they see Messiah falling and are rescued by Athrun. It's in the final minutes where we finally see Shinn meeting Kira again and accepting to work together for a better ending that we get a happy ending.