Mine would be these three:

1- The Spiderman/Doctor Octopus fight on the New York Metro Rail Train.

2- The Batman/Joker fight in the Gotham City church steeple from the Michael Keaton batman.

3- Johnny Storm using all four member powers (a.k.a. Super Skrull type) to battle Doctor Doom in FF2.

Wolverine & Sabretooth vs Deadpool: Wolverine Origins - Regardless of how you feel about the treatment of Deadpool in this movie, this team-up between Wolverine and Sabretooth was pretty sweet.

Iron Man vs Afghani terrorists: Iron Man

Iron Man vs Thor vs Captain America: Avengers

Batman jumps the river in his car to help Gordon who is "all alone" In Batman Begins.

That's the secret Captain. I'm Always Angry---Avengers

Spider-Man saves Mj and the Tram of people while the Goblin attacks. New York Rallies to help.---Spider-Man

Superman Vs Zod, Non and Ursa from Superman II
Michael Keaton whispering "I'm Batman" after beating up two muggers on a rooftop at the start of the first Tim Burton Batman movie.
Sinestro puts on the Yellow ring mid-way through the end credits of Green Lantern.

Great list!!

Howsabouts

Joker versus Bruce Wayne in Vicki's apartment--Batman

Batman interrogates Joker----Dark Knight

Octavius' sacrifice-----Spider Man 2

The fight in Vicki Vale's apartment is great. Michael Keaton's Bruce Wayne has a real quirkiness about his performance I've always liked.

And Octavius's sacrifice? I'd forgot about that scene. Very emotional.

Hard to pick just three, there are so many good scenes. Even if some of the movies that weren't that good.
All great choices so far.

1) Superman's debut in Metropolis, catching Lois and the helicopter in Superman: The Motion Picture. ("You've got me?! Who's got you?!")

2) Sinestro's speech to rally the troops on Oa in Green Lantern.

3) The Thing telling Susan Storm what he wouldn't give to be invisible in The Fantastic Four.

Honorable mentions: Joker's pencil trick in The Dark Knight, Tony Stark's test trials in Iron Man.

Excellent topic! I'm going to stick with the modern-age (post-Blade) films.

1: X-Men (1999). Wolverine's introductory scene in the bar, specifically when he pops his claws for the first time. Waiting a good fifteen years for this moment, seeing it on the big screen, slow-mo, and having Bryan Singer be able to get Hugh Jackman to tap into Wolverine's seething rage. This was the moment that I knew the dark ages of Marvel movies was over.

2: Spider-Man (2002). After Peter Parker finds Uncle Ben, and his sadness turns to righteous anger. Camera follows Peter as he runs down the alley (while putting his mask on), leaping onto the wall, crawling around a bit, flipping until finally resting on the flagpole (or was it a gargoyle?). The score that complements this scene adds perfectly to the tone. Again, waiting years to see this moment on the screen--and it was perfect.

3: Daredevil (2003). Bar Fight Scene. Any Daredevil fan knows that DD had the habit of busting up bars throughout most of his run in the 1980's. Whether you loved or hated this movie, you can't deny it was awesome to see his traditional bar bust-up translated to the big screen.

Honorable mention because it's not specifically a super-hero film, but it's actually #3 in the list (for me):

Transformers (2007). Intro scene with the Decepticons laying waste to the military base. Transformers 2 wasn't that great, and 3 was only somewhat better. In fact, all the coming TF films can suck, but we'll still have the intro to the first movie. Once again, waiting years to see something like this on the big screen, and it was executed perfectly for the opening shot, right down to the traditional sound the Transformers make when they change shape. This was pure excitement and wonder when seen for the first time on the big screen.

Too hard to pick just 3 so I'm gonna pick 3 scenes from Marvel movies and 3 from DC.

MARVEL

Spiderman 2 - Spidey's battle with Doc Ock on the NYC train.

Incredible Hulk - Hulk vs. the Abomination in downtown NYC.

Amazing Spiderman - Spiderman and the Lizard sewer scene.


DC

Batman (1989) - Batman vs. the Joker's thugs in the Gotham alley.

Green Lantern - Sinestro puts on the yellow power ring.

Superman Returns - Superman carries the huge chunk of new Krypton from the ocean into space.

I can think of a lot of scenes from other movies I like.

IRON MAN 2: TONY STARK vs JAMES RHODES "Gimme a fat beat to beat my buddy's a$$ to..."

PUNISHER: Frank Castle vs The Russian.

AVENGERS: HULK vs LOKI...although that's a short one. lol

+1 although I'd tack on the Hulk vs Thor in Avengers: Hulk side-punches Thor off of the giant fly beast they'd just struck down together.

I had to change the SUPERMAN ZOD fight to the PUNISHER vs RUSSIAN fight. I forgot about that one. It's one of the best and most brutal IMO.

Off the top of my head:

1. The Cap/Thor/Iron Man confrontation, when they stop fighting and look at each other. Avengers.

2. The upside-down kiss in Spider-Man.

3. Hit Girl vs gangsters Kick-Ass.

4. The Comedian on the grassy knoll in the opening credits of Watchmen.

5. "Back in Black" the opening scene in Iron Man.

HIT GIRL vs the Gangsters. +1. Great fight scene.

This list is hard to beat. The Joker scenes in Batman were awesome, but the "I'm Batman" scene was the most memorable for me. I remember feeling vindicated because Batman was finally depicted as a serious character.