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.
When you 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 always brings a tear. 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.
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.