At the end of the Negative Zone mission when both the Pro- and Anti-Reg forces put aside their differences and rejoin to fight the Fold. Features an especially awesome moment for Iron Man when he tells Hill, who's all set to arrest the beaten and weary Anti-Reg heroes, that if she has a problem with it, she'll have to go through all of them.
In the first game, a lone, unnamed Arsgardian Guard was facing down an army of super soldiers. He then hefted his axe and charged head on at the army of massive, hulk-like soldiers while screaming "For Asgard!!!". He sent more than five Super Soldiers flying in a single swing.
Loki deliberately throws a fight to trick the heroes into freeing the Destroyer for him, which he promptly takes control of.
Not to mention Thor's reaction to being hit by one of Doom's robots in the first game and his blasting said minion afterwards.
Plus Cap taking down several robots easily. Spider-Man was stunned.
A PC mod that gives you the DLC allows for a big one in Mephisto's realm: having Magneto in your party after the battle with Blackheart allows you to avert his sadistic choice and save both Jean and Nightcrawler.
Magneto: Calm yourself, X-Man. These cages may come from another dimension, but they are still made of metal.
When the team first boards the Shi'ar battleship, they're immediately confronted with an enemy who raises his weapon at them, shouting "Surrender now!" Just a split second later, Corsair attacks said enemy from behind and One Hit Kills him.
Taking down several deities, including Blackheart, Mephisto, Loki and Doom with a team of Badass Normals.
The final showdown with Dr. Doom.
The cutscene in the first game titled "Escape From Castle Doom", has Nightcrawler attempting just that. He uses his mad teleportation skills and a pair of swords to defeat a dozen Doom-bots in the most epic ways possible. It's definitely a scene worth watching over and over, just because of its sheer awesomeness. That's what training in the Danger Room gets you.
The cutscene in the first game, showing the last stand of the remaining heroes of Earth - Gambit, Shadowcat, Magneto, Charles Xavier & the frigging Hulk have all fallen at the hands of Doom; but Colossus, heavily mutilated & likely to die the moment he shifts out of his metal form due to blood loss, crawls and grabs Doom's ankle, if only as a sign of defiance. Doom pulls him into the air telekinetically, so Colossus spits in his face, prompting Doom to smash him into pillars. Cue Cyclops, the only other hero still moving optic blasting Doom with all he's got to try & save Piotr. Almost makes up for him not being in the game.
Doom effortlessly taking out missiles with the Odinpower.
A meta one- Captain Amercia and Iron Man's Fusion Move (Iron Man blasts into Cap's shield, which he reflects into baddies) making it into The Avengers movie.