I really like that mission in Freespace 1 when you lead that attack to capture the Shivan warship commanding four wings of GTA fighters. It was just the first time I REALLY got a sense of not playing alone and having to depend on your wingmen for survival. It was like "Beta and Charlie take out the fighters, Delta hit those turrets, Alpha you stay on my wing we're going straight in...". At least that's what I was telling them in my head

In Derelict there's that big battle in Phi Eridani where you're blockading the node and holding off the Shivans. It was just a -desperate- battle when I played it. Very memorable.
And how about that fantastic moment in Blue Planet when you jump in right above the Lucifer fleet to turn the tide of your "dream" battle? That was just epic. I loved, capital LOVED the sensation the moment you come out of subspace, see the planet below you, see the Shivans, see the GTVA warships, and realize you'd seen it all before. It was so well done.