2nd Runner Up: Having stupidly thought "Flying through this trench on Kilrah is annoying and boring. Why don't I just try flying straight there?" and becoming drowned in Ekapsis, after a painful battle with Hobbes and Thrakhath, ship shot to hell, still far away from the Temblor fault, when my college roommate, who was watching me, asked: Why don't you just use that cloaking device thing again? (me through gritted teeth as I dodge an Ekapsi): "Because I already used it. You can only use it once." (him): "Are you sure? Can it hurt to try?" (me, amazed and relieved) "Ooooooooo....."
1st Runner Up: WCIV. The Vesivius, just about to reach the Sol jump point, detects the pursuing Intrepid. Tolwyn orders her to turn around and engage with the cold, but awesome, line "Sometimes when you have a junkyard dog snapping at your heels, it's best to turn around and kick it in the teeth." Cut to the bridge of the Intrepid, where a horrified Sosa exclaims that the Vesuvius is turning around, and Blair, barely controlling the panic in his voice, calls out "Battle Stations!" as the camera zooms in for an extreme close up.
That moment gave me chills.
All time greatest moment: WC1, a mission in SM1 (or maybe SM2?) The Claw is about to be ambushed in an asteroid belt, and I'm ordered to fly a roundabout patrol and ambush the ambush. I get there and find swarms of Gratha, and maybe a bunch of other ships as well (memory is hazy). After a pitched dogfight where my wingman gets so beat up I order them home, dodging rocks and Gratha fire in my Raptor, I finally beat the last fighter (by afterburning towards him, whipping around, and launching my mine, and then tapping my burners again---my inertia carries it into him. Years later I will realize that this is Seether's "move of a true master"). Missiles gone. All guns down except for a single neutron gun. Shields out. Armor stripped bare. Powerplant damage: heavy. Ion driver damage heavy, top speed down to about 150 kps. Nearly out of fuel. Targeting computer: practically inoperative. Comm systems: nearly inoperative. Acceleration absorbers destroyed. It takes me about seven minutes of continuously hitting C-1 to get my comm system to work enough to get clearance, and I limp onto the Claw's flight deck. But I wasn't about to eject to end the mission. Never have I loved a ship so much as that Raptor on that day. Damned fine fighter.