Brainwashed Nightcrawler utterly curb-stomping the Secret Service to get to the President. Obviously it's not something he has control over, but it looks pretty cool. It's even backed up with Mozart's ''Dies Irae''.
Cyclops fighting the security guards is a really cool moment. Taking out 3 or 4 well trained guards in a matter of seconds without even using his optic blasts on all of them proves why he leads the X-Men.
The first time Wolverine stabs one of Stryker's soldiers right through the chest. Until that moment, a lot of people were expecting Movie Wolverine to be sort of like Animated Wolverine, who doesn't really do that to living people (and which he never really did in the first film). Once it became clear that this version of Wolverine had no problems slicing living opponents, fans could truly anticipate the badassery to come and we got it in spades when Wolverine roars into Stryker's goons with an animalistic berserker fury.
Logan: You picked the wrong house, bub!
Colossus throws two soldiers through the wall after turning to metal and No Selling their shots.
Marie, Bobby and John are trapped by a squad of Stryker's black-ops commandos. Enter. The. Wolverine.
Logan:rrrrrrrRRRRRRAAAAARRRGGGGGHHHHH!!!!(Leaps down from the mansion's staircase landing and piles the military boys under three hundred pounds of muscle and adamantium. They're sliced and diced in the tussle. Two more show up behind Logan with guns raised. Without even looking, he impales their lower legs, lifts them back and through the air for a twelve foot double body-slam and sheathes his claws in front of the awed X-kids!) Let's go!
Erik making his escape from his plastic prison. The little smirk on his face when he senses metal in range of his abilities for the first time in months, backed up by Ian McKellen's masterful dialogue delivery. A very squicky and highly memorable death, certainly one of the better Mook dispatches of all time.
Laurio: Have a nice sleep, Lensherr?
Magneto: There's something different about you today, Mr. Laurio.
Laurio: Yeah, I was having a good day.
Magneto: (gets up) No, no it's not that...
Laurio: Sit down.
Magneto: ... No.
Laurio: (draws his truncheon) I said, sit your ass down!
(He starts for Magneto, who holds up his hand. Laurio stops forcibly)
Magneto: What could it be...?
Laurio: (gasps) What - are you - doing?
Magneto: Ah, there it is... (He widens his palm, and Laurio lifts into the air) Too much iron in your blood! (He rips a cloud of red iron particles out through Laurio's chest capillaries, and squeezes them into a set of ball bearings. Laurio collapses in a blood-soaked heap.)
Magneto: Mr. Laurio, never trust a beautiful woman. Especially one who's interested in you.
Wolverine faces Stryker's men alone after closing the secret passage behind Rogue.
Nightcrawler saving Rogue via no line of sight teleportation when she gets sucked out of the Blackbird and is falling twenty thousand feet! Plus Magneto catching the entire thing just before it hits the ground.
For Mystique, when she infiltrates Stryker's base disguised as Logan, slips her cuffs, kicks ass, uses human shields, somersault's around gunfire and then flips them the bird while she slides under the blast-doors.
Mystique!Stryker: There's a meta-morph loose in the base! Could be anyone!
Control Room Operator: Anyone?
Mystique!Stryker:(Seizes one dude's assault rifle barrel, knocks him and the other dude out with lazy grace and seals herself inside.)
The bit where about a dozen heavily armed troops are stationed in front of Cerebro to prevent Magneto from coming through. Before they even see him Erik uses his mastery of magnetism to rip every pin out of the multiple grenades that each of these Mooks are carrying... Boom.
Logan's penultimate confrontation with Colonel William Stryker. Brian Cox and Hugh Jackman's acting is fantastic and the performance riveting. Although Origins added a bit of meat onto his character's bones, (considering Stryker flips between the fatherly general of an experienced soldier to a man petting his run-away dog.) We can't be sure of his true intentions to Logan; except of course when he tells his old war buddy to abandon the X-men. To which Jimmy Howlett replies with a frank Shut Up, Hannibal!.
The scene also masterfully shows why the bone claws are useless from a story perspective. Weapon-X was about dehumanizing Logan. The knives that burst from his hands turn him into something worse than an animal. They make him seem like a mindless, clinical instrument of death. A monster. But the following dialogue shows which man has truly changed his ways.
Stryker:(Screams horribly as Logan stabs him through the upper arm.)
Logan:(With justified relish.) How does it feel, bub?
Stryker: (Voice ragged with agony.) Why - did you come back?
Logan: You cut me open! You took my life!
Stryker: You make it sound like I stole something from you. As I recall it was you who volunteered for the procedure.
Logan: ... Who am I?
Stryker: You - are just a failed - experiment. (Cries out again as Logan twists his wound.) If you really knew about your past... What kind of person you were... The work we did together - People don't change, Wolverine. You were an animal then, you're an animal now. I just gave you claws. (Alarms from the base start to blare.)
Logan: What the hell is that? What is it?!
Stryker: The dam's ruptured. It's gonna flood water into the spillway. It's trying to relieve the pressure. It's too late. In a few minutes, we'll all be underwater. Come with me and I'll tell you everything you want to know. You can't help your friends, they're as good as dead, Wolverine. You're a survivor. Always have been. (Lopsided smile.)
Logan: Oh, I thought I was just an animal... With claws... (Pops second set of adamantium blades slowly but surely inching them to Stryker's face, who tries to feebly arch out of the way without much success due to being pinned to the chinhook.) If we die. You die. (Ties Stryker up with the mooring chains and runs back to save his friends.)
Stryker: Aah! There are no exits that way, Wolverine!
Rogue piloting the jet during the finale. Also, earlier, when she stopped Pyro (who was still her friend at the time) from rampaging.
Pyro's rampage, at least until it goes too far, is awesome in itself. Considering the one idiot cop overreacted and shot Wolverine, they had that beating coming.
Honestly, just the fact that a major studio made a blockbuster sequel that was not only good but many people view as even better than the original is a CMOA for Hollywood.