The Fastball Special executed in the first moments of the movie, taking off the head of a Sentinel without breaking a sweat, and Wolvie lighting his cigar on the flaming debris.
Though he was only in the movie as what amounted to an extended cameo, Angel unfolding his wings (with an accompanying score) nonetheless stands out. Points go to Dr Rao looking absolutely awed as she sees them unfurled for the first time.
And then his Big Damn Heroes moment in the climax where he arrives just in time to save his father from being chucked off the roof
Storm frying Callisto on a chicken wire fence with her lightning. And Callisto's lip stud glows for a minute afterwards.
Iceman fully "ices up" for the first time and takes Pyro down by headbutting him.
Beast, everyone's favorite blue, furry, and extremely eloquent doctor drops his lofty nature and basically eviscerates the baddies. "There comes a time when all men must — Oh, you get the point!"
And of course, when he stabs Magneto with the cure while he's distracted by Wolverine.
Heck give credit to Wolvie, it was his idea. The fact that Magneto never saw it coming, thinking Wolverine was trying to rush him, is icing on the cake! And very satisfying for all the curbstomps he put Wolverine through in the series.
Heck, Beast in general. We all knew Kelsey Grammer could bring the appropriate erudite elegance to the role, but who knew he'd be able to pull off Beast's physicality and savagery as well?
Topped almost immediately by Kitty Pryde, who owns him beautifully.
Humanity is no longer the pushovers of the first film, nor the outright villains of the second. By the start of the film, they've managed to capture Mystique, Juggernaut, and Multiple Man, and treat them with the respect they deserve. Afterwards, they're smart enough to ditch absolutely everything metal when gearing up to fight the Brotherhood, and during the final battle, the soldiers have no hesitation fighting alongside the X-men and following Wolverine's orders.
The encounter between Wolverine and Magneto in the middle.
Wolverine: I'm not leaving here without her. Magneto: Yes, you are. * Magneto throws Wolverine across the entire forest*
Subverted beautifully later when Wolverine charges at Magneto during the battle for Alcatraz. He charges at Magneto, who taunts him as he disables him (again). Only for Wolverine to smile.
Magneto: (feeling cocky) You never learn, do you?
Wolverine: ...actually, I do. (Beast jumps Magneto from behind and injects him with the Cure)
Magneto: (in shock and horror as his powers begin to fade) I'm...
Wolverine: One of them?
The best part? It's a Call-Back to the first movie, when Magneto said the same thing to Kelley after he'd turned him into a mutant.
Part this, part Crowning Moment Of Characterization, but: the Professor has died by Jean's hand. Pyro says he only wishes that he could've been the one to kill him, since it would be one more thing out of the way of their conquest. Magneto whips around and cuts him off mid-sentence to say that his greatest regret is that Xavier will not be joining them, and no one will speak ill of him. There's a kindly, grandfatherly, yet terrifying look on his face that firmly states that the next ill word of Charles Xavier that passes Pyro's lips will be his last.
Magneto lifting the Golden Gate Bridge.
Not to mention his attack on the prison transport. To crush cars and fling them to the side with mere hand gestures is but a simple task for the master of magnetism.
Juggernaut's No-Holds-Barred Beatdown of Wolverine is one for both. For Juggernaut, displaying levels of physical prowess never seen before in the series. For Wolverine, he never stops coming at someone who he doesn't have a prayer of defeating.
Wolverine's general increased badassery in general. For the first time in the series, he is actually defeating someone more than fodder mooks straight-up.