Though I especially liked the Prelude, the Kilrathi missions, Zero Hour (10B), fighting the Devil Rays in mission 9, and of course the infamous Simulator Mission 9 : Treacherous Nebula. I've managed to finish it with the Banshee, Bearcat, and Ferret. Definitely one of the hardest WC missions ever - speed is pretty much everything. You'd better fly a fast fighter and be *very* quick, or else you're likely to get blown up in a second.
I really liked the Confed gauntlet too... Fighting Vampires is fun. Out of curiosity, has anyone managed to finish at least one of the gauntlet missions without cheating? I sure couldn't.