This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Virtue's Last Reward
Learn about Tenmyouji's past and identity, then just try to maintain composure when you realize the identity of the old woman.
"The Akane Kurashiki I knew isn't there. She isn't anywhere..."
In what doubles as a Crowning Moment of Heartwarming, the password of the old woman is Jumpydoll. "Jumpy" was Akane's nickname for Junpei when they were children, and her most treasured possession was the doll he gave her as a parting gift. Akane never forgot about Junpei, even after all those years. And according to K, she wished nothing more than to marry Junpei and live with him. But she can't. Notice that she told K that when she was already much older. So yes, she never forgot him.
Luna's ending, especially when Morphogenetic Sorrow (the theme of the final puzzle from 999) begins playing during a flashback.
Luna: I watched six people die and did nothing. I deserve this.
Sigma: No! No you don't! Even if you had done something, you would have been killed anyway! You can't blame yourself! You did what you could, you're not wrong! The game is what's wrong! Forcing you to watch your friends die is what's wrong!
Luna: Oh Sigma... Thank you. I'm... I'm really glad I met you... At least I get to die in your arms...
The ending line of the scene is especially heart wrenching:
With one last, quiet chime, the music box wound down. I was left with nothing but silence and the cold pool of tears over my heart.
Even more so when you look back to K's ending: K was saying how Zero Sr. created a "robot mom" for him. That robot's/GAULEM's name was never stated in K's ending, but is confirmed by Word of God to be Luna. Suddenly "It looked sad, but it was only programmed to look that way" from K doesn't sound so convincing anymore... And part of the reason for Luna's loneliness is explained.
And then everything becomes even worse when you take both this and Word of God information into account. Another topic that wasn't fully explained by K was that his father in his youth was in love with a woman according to the old woman, but K didn't seem to know anything about said woman. We learn however from Uchikoshi that Luna's design and character was based on a woman Zero Sr. connected with and that Luna wasn't actually created to give K a mother, implying she had already existed before the request. Now recall that Luna calls herself "a jumble of metal and plastic that pretends to be real" and suddenly, the line makes a lot more sense.
What about Snake? Clover's esper abilities are being absorbed by the other, more powerful psychics in the group, not to mention she's forty-five years ahead of him, assuming he survived the Radical-6 outbreak and the antimatter holocaust. To him, his sister blinked out of existence one day, never to be seen again. Even if the events of the End or Beginning path come true... what about all the other Snakes whose Clovers never come home?
No, really, let that sink in for a minute. To Snake, Clover has gone missing and is probably presumed dead. Given what we know about their relationship both from 999 and from what Clover tells us in VLR, how protective they are of each other after being put through two Nonary Games and the way he absolutely snaps in 999's Safe End timeline, when he learns Clover is dead, the chances of him surviving something like the Radical-6 outbreak seems slim at best.
And you just try and picture Snake or anyone from the first game either succumbing to Radical-6 and killing themselves or living through that nightmare and having to survive in a post-apocalyptic wasteland without getting emotional.
Thankfully, the Golden Ending gives this a bit of a Hope Spot in the form of Akane exploiting Schrodinger's Cat to possibly send them back into the past, body and all.
The Game Over cutscene of the Normal End of the game if you fail to disarm one of the bombs. Right as the bombs are about to explode, Phi falls into your chest and thanks you for always standing by her, while Sigma vows to go to the past and make things right.
The K ending. According to Word of God, K, who on this path is Sigma's clone/son Kyle, was the one who broke Dio's bracelet, preventing himself and Phi from going through the white door. He knew that Sigma, his father, would only be able to save one of them from the bracelet penalty with the neostigmine, and wanted to see if Sigma would choose him, even knowing that Sigma's 22-year-old consciousness would not remember him. But Sigma chose Phi. Even though it was apparently out of necessity, since Sigma didn't know that K's armor was unlocked, one can only imagine how that made Kyle feel.