1. Freespace- Taking Down the Lucifer
This battle is the last one in Freespace and probably also the most unique. Up until this point in the game, the Terran forces and their Vasudan allies have basically been at the mercy of the Shivans. The biggest factor in their defeat? The impervious shields of the Lucifer: a massive Shivan destroyer that's kicked the hell out of everything stupid enough to get in its way. After a devastating attack on the Vasudan homeworld, the Lucifer turns its eyes toward Earth. There's hope, however. Your forces discover that the Lucifer can't activate its shields in sub-space, giving your fighters a slim chance to destroy it.
This mission, for me, was the embodiment of what I enjoyed most about Freespace: its scale. While taking the Lucifer down is actually somewhat easier than many of the other missions in the game, the sensation of getting up alongside this behemoth warship is incomparable. It feels like a big deal just through size alone. Add in a time constraint and the narrative's high stakes and you're given a mission that's intense through the virtue of its sheer spectacle.