Frosty: I'd have to agree with you. Maybe because in WC3 you're on the Victory for the entire game (except for those last few missions, of course), getting to know your wingmen and the like. It felt like "home." I had this same feeling with WC1 and 2, as well, but in WC4 you're running all over the place, changing wingmen and ships and such.
Or something like that.
I don't know if I have one favorite, but here are some scenes I like:
I always like that scene at the end of WC1 after you blow up the Star Post in Venice (eh, is that right, it's been about a year since I last played WC1
), where the Confed soldiers raise the flag ala Iwo Jima. I always thought that was really good, and the end scenes for SM1 and 2 were also pretty kick ass, with the Emperor having Prince Gilkarg executed and the Firekkans waving their weapons defiantly at the departing Kilrathi ships. Those were some good endings (better than WC2's "Three cheers for Colonel Blair" ending, IMO).
Eisen ramming the Kilrathi ship during the WC3 losing endgame was also pretty great, and I enjoy the scene of Blair dropping the T-Bomb in the PSX version (although I'm still not sure what he says to that Kilrathi who fires on him), and then two other scenes in WC3 I really enjoyed: Thrakhath's broadcast to the Victory and Angel's death scene, of course.
There were a bunch in WC4. The first three opening scenes (attack at Hellespont, the bar in Nephele, and the Assembly) blew me away, as they were the first images of Wing Commander I'd ever seen (aside from a part of a WCA episode the previous year). Seether blowing poor Kyle Lee away, the first defection (when the Intrepid's deck is one big mess), Vag's death, the scene at the hospital on Telamon, the Axius base scenes, when Eisen showed up with the St. Helens, and the standing ovation Blair gets after the Assembly votes against war. That's a hell of a lot, and there are much, much more, but those are the few that stand out to me.
Really, the only two scenes that stand out in Prophecy to me are a.) when Casey has the image of Blair in the Bugs' grasp in his mind and b.) those scenes with Blair in the tower toward the end. Everything else was pretty ho-hum, IMO.
Whew! That's a lot!