Homeworld/Awesome

Homeworld
"Bridge Officer: The cryotrays are under attack. Defend them. ... These ships are different than the ones we encountered at the Khar-Selim. It is likely they were involved in the destruction of Kharak. Capture at least one vessel for interrogation, and destroy the rest."
 * Saving all the cryotrays in the third mission. These are the last remnants of your entire civilization. One hundred thousand souls are crammed into each tray. You can hear the undertones of heartbreak turning to anger in the bridge officers voice as he issues the mission orders.


 * From the end of that same mission, just five words: Subject did not survive interrogation.

Cataclysm
"Captain: It doesn't matter how we die! One ancient monster is as good as another!
 * The Kuu-Lan's captain arguing with the Bentusi while battling them. You read that right: the captain of a mining ship battling the Bentusi. And not just one but SEVEN tradeships AT ONCE. He knows it's completely futile but he refuses to back down and run away because the alternative will definitely be a Fate Worse Than Death; instead, he bares fangs and teeth and hurls insults at the Bentusi, calling them the galaxy's biggest hypocrites for running away and letting everyone be consumed by the Beast while still calling themselves the good guys. And the Bentusi get so ashamed of themselves they actually back down from the fight. I mean, holy shit.
 * Just for reference: no one in recorded history ever engaged a Bentusi tradeship and lived to tell the tale. This guy did.

Bentusi: We... are... not... monsters...

Captain: Aren't you...? Look around! Look what you've done to our fleet! All because we dared to stand in your way! Look at yourselves: the aloof and mighty Bentusi! Slaughtering the people who ask for your help! You're worse than the Beast!! AT LEAST THE BEAST DOESN'T PRETEND TO BE RIGHTEOUS!!!"

Homeworld 2
"Karan S'jet: Sajuuk has returned."
 * The last-minute return of the Mothership/Sajuuk Fleet to Hiigaran space in the final mission of Homeworld 2. You can see the last remnants of the Hiigaran defense fleet who stayed behind to protect the planet from the Vagyr getting chewed up by a huge Vagyr onslaught. They've been pushed to the final defensive line, directly in orbit over Hiigara. Then the screen cuts to your fleet jumping in. Cue Karan, calmly announcing the arrival of a legend and the total reversal of a Curb Stomp Battle:

Homeworld

 * A choral version of Samuel Barber's Adagio for Strings, potentially one of the saddest instrumental pieces ever written, plays during the launch of the Mothership (giving a spiritual "we're putting our whole race's effort into this" feeling), as well as two other highly dramatic moments, potentially bumping the first one up to Tear Jerker status and serving as a Theme Music Power Up for the second one, at the end of the final mission, as enemy rebels courageously - suicidally, in fact - charge straight at their Emperor to clear a path for you to attack.
 * The song "Homeworld (The Ladder)" by Yes at the end credits.
 * The Taiidan Empire's theme. It's subdued and threatening--and the herald of another Taiidan fleet coming in. It makes you crack your knuckles and prepare to fight your Worthy Adversary.
 * The Turanic Raiders' theme. Ominous and sinister in equal measure, with a lazy snakelike tempo that suits the predatory mercenary/scavenger culture of the Turanics well.
 * The Kadeshi battle theme. Slow, and with a lo-o-ong buildup, but VERY menacing, and it fits them perfectly. You aren't taking revenge on the Taiidani or routing pirates. You're just trying to get out of the nebula alive.
 * Much of the ambient music, the original game particularly - the Garden of Kadesh, Super Nova Station, Garden View, Bridge of Sighs - though rather slower.
 * Here is a combination of some of the best pieces in the game.

Homeworld: Cataclysm

 * Cataclysm had a couple: The Battle for Hiigara from the first scene, a simple, calm, totally epic piece for an equally epic scene, and the main Beast theme. Also, you know truly how screwed you are when you're fighting the friggin' Bentusi.

Homeworld II

 * The Planetkillers' theme. Slow, mournful, and almost hymnishly solemn, quite fitting for a situation where a slipup.
 * Also the rather climactic Battle for Sajuuk theme and the version used in the credits.