- Agnus Dei, 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. It also plays during the mission where you save the Bentusi, and they share with you a recording of your ancestors' exile from Hiigara.
- 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.
- It's completely unlike anything else in the game, but the credits song makes a damn fine victory anthem.
- 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.
- The Planetkillers' theme. Slow, mournful, and almost hymnishly solemn, quite fitting for a situation where a slipup could get your planet fried.
- Also the rather climactic Battle for Sajuuk theme and the version used in the credits.
- The Keeper is aware. The Keeper understands. The Keeper has seen the enemy.