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.
There is also a somewhat minor one that slips past the radar of many every now and then. The mission where you save the Bentusi, and they share with you a recording of your ancestors' exile from Hiigara, all while being accompanied with Agnus Dei, the choral version of Adagio for Strings.
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.