The three kryptonians wade through White House security as if it were a fun passtime in Superman II. When Zod tries out the machinegun, it seems as if he's just curious to see how it works. Awesome.
The opening "Bloodbath" scene from Blade. Vampires, techno music, blood and ashes. That scene alone spawned the next 2 sequels.
The fighting climax between Batman, the Phantasm and the Joker at the end of Batman: Mask of the Phantasm. The big reveal, the huge fight, Mark Hamill giving a great vocal performance as the Joker. I can picture the whole fight if I close my eyes.
I'm gonna take one from the list link, the "Okay, put more." scene from Unbreakable. *shiver*. Best moment in an Origin story. Ever.
Black-costumed Spiderman comes to settle the score with Harry Osborne. Not exactly the greatest movie ever, but the Peter-Harry relationship culminates wonderfully, and was the the only organic plot in the whole 3rd film.
Cyclops: "Prove it!"
Wolverine: "You're a dick."
Also from X-Men, the standoff between Magneto and Xavier outside the train station has a great sequence of escalation. Mags wins out in the end, but possessing Sabretooth to threaten to rip out Magnus' throat was really cool.
Another from the linked list, the "He's just a kid." scene from Spiderman 2. Added to that the "You'll have to get through me." scene right after it where they all stand up to Doc Ock on Spidey's behalf, only to be whacked out of the way as a afterthought.
Elasti-Girl infiltrates Syndrome's base in the Incredibles. So cool, and it was a toss-up between that and the "no capes" flashback from the same movie, but there was more drama in the sneaking in.
The Iron Giant grumbles out "Su-per-man" as he flies off to sacrifice himself and save the town. Lump in throat, tears welling, true hero stuff.
"Some days you just can't get rid of a bomb!" - Batman: The Movie
Bullseye kills an old lady with a peanut. - Daredevil
The Beast meeting Leech for the first time and is just completely emotionally torn by how it made him feel. - X3