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
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.
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.
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.