I've only read the Gundam Seed manga, and it kicked total ass. I especcially liked all those outer and inner conflicts of Kira. He battles day in, day out, in sleep and when awake, with very few people actually listening to him and caring, despite all the work he puts into everything.
But my favorite cahracter is still Flaga. His ship, the Moebius Zero, reminds the hell outta me of Axelay.
And, of course, Lacus Clyne is always an unforgettable character, even if you exclude those nicknamed the same.
But that's just the manga. I haven't seen the anime, but I desperatly want to.