Malachor, the final world of Knights of the Old Republic II, was incredibly emotionally affecting - it felt like the last echo of the end of the world, (and it was indeed the end of the game).
Kreia stating that in the Exile's memories, they can no longer picture the beautiful world Malachor was before they dropped the superweapon on it, instead, it's always the desolate landscape that they caused.
The intended version would have been much, much worse, with the Exile's companions confronting Kreia on their own only to be beaten down and imprisoned in order to force the Exile to choose between freeing them and making the final boss fight harder, or allowing them to die for an easier boss fight. Meanwhile, Atton manages to escape capture only to sacrifice himself in a one-on-one battle with Darth Sion - and if he loses, Sion tortures him and leaves him, broken and dying, for the Exile to find. The audio file for Atton's death exists in the game's files, and it is heart-rending.
Atton: Hurts... when I laugh...
Oh, god, that one file had me sobbing. I always loved Atton's character; when KOTOR2 goes Darker and Edgier, Atton is a consummate Deadpan Snarker, always making the situation funnier with his humor, yet never appearing to be outright comic relief. Then, you get to this, and he's just sitting there, dying, and when he laughs, trying to ignore the pain, it comes back a thousandfold.
Considering Atton's back story as a former Sith assassin, dying for fighting a Sith Lord could also be interpreted as a Redemption Equals Death moment, especially if he has been turned to the Light Side via the Exile's influence.
Seeing Remote being destroyed. It's so sad to see Bao-Dur losing his best friend. It's even worse since it has been confirmed that Droids have no afterlife.
Although it is possible that Remote doesn't die. Nonetheless it's still crushing that Bao-Dur's future is never revealed. Made even worse given that Kreia embellishes on the future of everyone else.
The Exile's brushes with Revan's love interests are truly depressing. What compounds this is the story so far from the MMO: both player characters apparently disappear from the known-galaxy to die seemingly-pointless deaths, never again seeing anyone they love. This may not prove to be the full story, but it's pretty gorram depressing. No K3 was bad enough, but seriously, what the hell?
Making this Troper's eyes roll hard is the comic book they were giving away with the MMO's demo. There's this hotheaded young Jedi named "Shan," and the Council is worried about "her heritage." Does that mean that they're going with the idea that M!Revan knocked Bastila up, skipped town without telling anyone, died alone, saddling her with a Someone to Remember Him By and the consequences?
Sadly, the Revan novel confirmes that Bastila was indeed pregnant with Revan's child when Revan left. Poor Bastila, for being forced to raise her child without ever seeing her child's father again...
However it's obvious that Revan only left to protect Bastila. He was prepared to sacrifice himself and leave everyone he loved behind to make sure it never got near Bastila and his child. And honestly, doesn't that sort of Heroic Sacrifice sum up everything about the redeemed Revan in a nutshell?
It's also very in keeping with his character. After all, Revan made the hard choice to defy his Jedi training and went to fight the Mandalorians because he knew that no-one else would step up otherwise. Revan never was one for sitting back and letting a problem remained unsolved and made the hard choices so no-one else would have to?
Carth's appearances, if Revan is established as female and Light Side, are particularly affecting. "There's just this emptiness where she used to be." It's enough to make you picket Bioware/Obsidian and demand KotOR 3 just to tie off that plot thread.
The meeting with the Exile at Citadel Station pretty well broke me. Carth spends the entire interview with his back turned to the Player Character, audibly trying not to lose it.
Hell, Raphel Sbarge managed to pull off LOTS of these. In the cut-content, female-only ending, Carth makes this Last-Second Chance/You don't want this life for yourself plea. Hear him out, and boy can he sell it. It's enough to make many an aspiring Dark Lady relinquish power for an Everybody Dies ending. Another bit of cut (and easily restored) content comes after the female PC finds out what she used to be. "Was everything you said a lie?" There's this hitch there, and I still feel a little stab in the gut when it's delivered.
Furthermore, you get his character in Mass Effect. Just you TRY leaving Kaidan to die...
As much as I liked the other character, I couldn't even countenance choosing her over Kaidan.
The music in the Jedi Enclave. And the visuals of what happened to the place sure didn't help.
There's also Kreia, moving to the benches. She has, from Peragus, projected the image of a cold and aloof mentor figure. She hid all of her pain from losing her hand on the Harbinger. Even discounting Gameplay and Story Segregation, she has fought alongside the Exile without protest and with the capabilities of the younger and more able-bodied crew. And then suddenly, she is unequivocally presented as bone-weary and old - you can feel every year she has and then some as she makes to sit down. It doubles when you remember that, after her hand was cut off, Atton tells the Exile that she seemed to not want to display any sign of weakness around the Exile, and then allows them to see this...
Might not be in the game, but the ending of Destroyer certainly qualifies. Zayne finds out that Chantique lied to him, and turns to try and make amends... only to see that Jarael is gone.
My eyes were brimming with tears in the middle of the following conversation with Hanharr in KOTOR II:
Exile: Why did you kill Mira?
Hanharr: Because I was the stronger. She was prey. Because she saved my life, and she would not let me take hers. So I tore it from her.
Exile: So she saved your life once?
Hanharr: She showed me mercy, and that I could not bear. To feel such, from prey. She had my life in her hands, her weapon pointed at me as I lay wounded in my own traps, and she did not kill me. And I saw her eyes. And I saw she felt... mercy.
Exile: So you would rather she have killed you?
Hanharr: It is the way of the hunt. When one lies broken before you, you end them. There is no mercy in such things - there is death. That is the price for the failure of the hunt, and she denied me that death. And that is what I could not bear. Yet I could no longer kill her, for it meant I owed her... owed my life to a human. Humans who broke all of my people with slavery - she did what they had done, to my people, to me. And that is why she had to die.
Exile: She did not make you a slave - instead, she denied you freedom, death.
Hanharr: You are wrong, human - those are not my words, nor the truth.
Exile: I think you wanted her to kill you, to break you. To end your life.
Hanharr: I do not chase death, I chase prey.
Exile: You have spoken of your tribe, Hanharr, and I think you wished to join them.
Hanharr: My tribe is no more - my people are no more, because of humans!
Exile: But you said they exist, but not here. And you wished to join them.
Hanharr: I... I see your eyes... hear your words, human. And your words echo within me. Perhaps I wished to die at her hands. And walk the Shadowlands no longer. Yet she spared me, and to continue living... I could not bear it. I wish to go where my tribe went, where I sent them, where they are finally free. Where they may forgive me. I do not wish to walk in the Shadowlands any longer. When I die, I want to walk on top of the trees of my homeworld, to hear the voices of my people again.
Exile: If you wish to die, then let it be done in a way that matters - saving others.
Hanharr: That is the only pledge I have heard from a human that I will accept. I will walk with you, human, and my strength shall be yours. I shall break our enemies. And when death comes, do not turn it aside - and I will do the same for you.
Exile: I swear the same - for now, until the end of our journey.
Hanharr: Then it is done - we die together, our lives as one, or not at all.
Juhani's distress and sadness at having killed her mentor always brings a tear. It's nice when she finds out she didn't kill her - it was all a character test.
A cut ending from the first game if the player is female and pursues the romantic option with Carth and chooses to return to being a Sith Lord. After killing Malak and preparing to destroy the Republic fleet, Carth will, somehow, make it to the bridge of the Star Forge where and Revan and Bastalia are and try to convince Revan to stop her fleet, also telling her he loves her despite everything. You can just choose to kill him, but if you agree, you kill Bastila (who is NOT pleased with the Love Redeems moment) and Carth admits that there's no escape for either of you. Lovers die together. After this you get the scene from the lightside ending of the Republic fleet destroying the Star Forge and Vandar Tokare question at what cost the victory came at, wondering where you and your crew are. Dead, you may have saved the Republic, but you and your whole party are dead now.
A meta example: LucasArts rushed the game for Christmas, causing Obsidian to leave out a lot of content. But when Obsidian offered to restore it all with a patch, LucasArts refused to allow them to make it! The lost content includes cut dialog, the Crowning Moment of Awesome that is the HK factory, a HUGE amount of the final mission, and interactions between Exile and his/her teammates. That LucasArts could so callously kick Obsidian like this makes me feel really down...