When you're about to deliver the rakghoul serum to the infected outcasts, three of them immediately mutate just moments away from being cured. It is heartbreaking to kill them knowing that you were just a few seconds late from saving them.
The destruction of Taris and Dantooine, especially once you see the sequels. Everyone you helped, hurt, or just talked to are gone. Three hundred years later, Taris is little more than a rakghoul infested swamp, the Republic efforts to rebuild it come to nothing, and the Empire swoops in and finishes it off. Plus, even the Hope Spot you get if you complete the Promised Land quest light side is turned into such an utter case of Shoot the Shaggy Dog that it's tempting to fork over the journals to Igear because that would have been a fast death for the poor bastards.
If you Do Well, but Not Perfect with the Sandral-Matale quest, the poor kids end off running off together, but their families cut them off and they end up taking refuge at the enclave. Made even more tear-jerking by the sequel. Apparently both families are wiped out in the attack, but Shen Matale managed to save several people before getting killed.
Mission trying to keep a brave face in the light of Taris's destruction. She provides the page quote for Player Punch.
Juhani's distress and sadness at having killed her mentor. It's nice when she finds out she didn't kill her - it was all a character test.
What makes this worse is that you can make a persuade check to convince her that she's forgiven. If you fail, she just sadly says that you're lying to her and waits for you to kill her. It's one of those things that really makes you want to hug her and tell her it's OK.
The fact that it was a character test makes what was done to Juhani, for many players, even worse. There were better ways. All that pain, the guilt and miserable self-hatred, all that suffering inflicted on a young woman who by her own admission was always alone among the Jedi, who only ever wanted to be good enough for them...and for what? To teach her a lesson? Juhani's master intentionally goaded her into attacking and then let her believe she was dead, for at least several weeks by the time the player shows up. She could have visited in person to speak to Juhani at any time and try to talk her down, explain what she did and why...and didn't. And no one ever explains why for all that time they didn't even bother to try. Carth even lampshades it if you speak to her in the rotunda afterward.
Carth:First the Jedi trick you into becoming an enemy, then they welcome you back as a friend. Can't say I approve of their training methods.
Not only did the Council know exactly what had happened the whole time and do absolutely nothing to help her, they blatantly use Juhani as a test for the brainwashed Darth Revan, just to see what they do. And if you choose to kill her...they don't really seem to care that much. And Juhani genuinely believes that it was all justified and entirely her fault.
If you do kill Juhani, there's a character (heavily implied to be her girlfriend) who calls you out on it. If you do it right, you see her again... at the Sith Academy, where she tries to kill you. So congrats; thanks to their method of testing, a promising Jedi is dead and another driven to the dark side.
Another Juhani one. you can encounter Dak Vessar, who was a Padawan alongside Juhani, and a friend of hers. He confessed that he loved her, but she couldn't return those feelings due to Incompatible Orientation, and apparently he didn't get the memo that she was a lesbian. She tries to plead with him that it really was a misunderstanding and she still cares about him, but he's too angry to listen. The best you get is him leaving the Sith and go his own way.
The end of the Kashyyyk quest. If you play Dark Side, you are leaving a thieving, petty, and cunning slimeball in charge and letting him continue to sell his own people into slavery. If you play Light Side, Zaalbar is stuck between his brother and his father, desperate and confused because he doesn't want either of them hurt. You can try to argue for peace, but Chuundar refuses.
If you fail to redeem Yuthura, but still be kind to her, she admits she doesn't want to have to kill you, but she has to try because that's just the way the Sith work, and that it's just best to Get It Over With.
Likewise, it's very easy to botch the Dustil quest, causing the kid to lose his temper and you have to kill him in self defense. Carth is completely devastated and apologizes for being a bad father.
Darth Malak of all people has a moment. Right before he dies he finally lets go of all his anger and lust for power and sadly admits that in spite of all his boasting, part of him always knew he was nothing but a pretender chasing a destiny that was never his and that in the end he never amounted to anything.
The cut (but easily restored) Dark Side female ending. Carth shows up after Malak is dead, saying that he somehow knew you would be victorious. Bastila is in full-on catty mode, sneering at you to kill him, but Carth pleads his case; this isn't the woman he knew and cared for and that if you continue down this path, it's going to destroy you. In the standard game, you just laugh in his face and kill him, but the cut ending has you turning on Bastila, and choosing to die on the Star Forge. You tell Carth to run, but he stands his ground, saying there's no other place he wants to be than here, dying with you. Again, it's Sbarge's voice acting that totally sells it.
One particular music track which can hit like a sack of bricks is Bastila's theme. You hear it first on Taris, and it's hauntingly beautiful, with notes of sadness and conflict - much like Bastila herself. And after Bastila's capture, you fight your way to the 5th star map, and reach the unknown planet with all it's dangers. You clear out countless Dark Jedi from the temple, then make your way to the upper levels... and the theme returns. Confused, you round the corner... and there she stands, waiting for you. Especially combined with the romance subplot, the sheer emotiveness of the music makes the sight of your former companion fallen to the Dark Side tragically moving.
On a related note, if you blow it with your persuasion checks on the Star Forge (which are quite difficult to make), you end up with Bastila pleading with you to kill her because she feels she is far too broken to return. She basically commits suicide via your lightsaber.
If you play Dark Side, the fact you have to kill most of your party. The one that hits hardest? Mission. She still insists there's good in you and that you won't hurt her. Bastila mocks her and she ends up dead by your hand. Yes, your Moral Event Horizon is killing a teenaged girl who did nothing wrong but believe you weren't past redemption. So, how are those Dark Side points? If you a complete and total bastard, you can order Zaalbar do kill her — which he does. He'll turn against you, knowing he'll probably lose, and Revan will mercilessly cut him down too.
The devastation of Serocco. We see it from the point of view of the Republic Fleet in orbit, as dosens upon dosens of mandalorian warheads ram into the populated planets, targeting cities of innocent people. There's no sound effect, just the visual of dosens of mushroom clouds rising from the surface. Zayne screams "The people! The people!", hide Jedi over the entire galaxy feels the pain of an entire people dying. Revan, systems away, can do nothing but whisper "I feel it".
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.