The sorrow in Iji's voice after her first few kills. "I'm sorry..."
The hair ribbons scattered through the complex that belonged to Iji's now-dead sister. Ir really makes it clear just how much Iji has lost due to the Tasen, especially when Iji realizes she's been hallucinating them.
If the player fails to obtain or take heed of the warning Iji senses from the hair ribbons, and the player similarly fails to exhibit precognition, Asha kills Iji's brother and Iji suffers a Heroic BSOD and goes on talking to him as if he's still alive.
The last stand of the Tasen. It's bad enough watching them be hunted down and slaughtered one by one by the deeply sociopathic Komato if you've been reading the various logbooks, but when they're driven to their very last holdout the conclusion is all the more painful because the Tasen diary writer and her girlfriend, and Vateilika, if they're still alive, are all holing up there, and if you've been on the violent path, before you can enter something tears through their defenses and butchers them all.
The ending and the death of General Tor is very heartbreaking.
ESPECIALLY the ending in which you don't save Dan from Asha. The entire planet is almost devoid of life, save for ants and plants, and the few humans, Dan is dead, and the Tasen are on the verge of extinction, if not extinct already.
The song used in the credits, "Further", originally by VNV Nation but the version used in the game is a cover by Life Force. While it wasn't written specifically for this game like the rest of the soundtrack, it might as well have been. The lyrics pretty much describe Iji's view of the entire conflict, and if you think of it as if she's singing to Tor after he dies, it becomes that much more powerful.