Quicksilver's entire plan in the his storyline debut is, quite simply, brilliant. By forcing the X-Men to save Senator Kelly from an assassination, he ends up making it look like they are the bad guys and not the Brotherhood.
When the X-Men tried to raid Genosha to find the Professor, Magneto effortlessly owns them. This being one of the few times outside the comics that Magneto (who's almost always an Adaptational Wimp) and the X-Men actually get into a fight, it's especially awesome. See for yourself.
One you might miss owing to Magneto easily kicking the X-Men's collective butts. Iceman reminds us that he's an Omega-Level mutant by being the only member of the team to actually land a proper hit, managing to destroy Magneto's helmet and freeze him in place temporarily.
Another one (partially for Magneto, partially for the writers) is that after years of Flanderization saying Magneto's only telepathic defense is his helmet, when Emma Frost tries a telepathic attack Magneto resists (at least twice as long as The Juggernaut usually does) enough to still be able to throw Wolverine into her.
Nightcrawler's first episode in the spotlight, when a refugee boat he is on is attacked by the Reavers, the adult mutants are kidnapped, and the children are left on board to drown. Kurt escapes, helps the children repair the ship, and sets off to rescue the adults. The Oh Crap look on Spiral's face when she sees the ship she thought she had scuttled pursuing them, with Nightcrawler standing at the bow holding a cutlass is priceless. The fight between Spiral and Nightcrawler shortly thereafter also qualifies.
Kurt: I'd be careful * drops arms* You don't have any more mechanical arms to lose.
Wolverine punching Bruce Banner in the face, causing him to become the Hulk and go mad on SHIELD again, after the truth about the WENDIGO project comes to light. Even having his ass knocked into the next county doesn't wipe the smirk off his face.
Rover, after having his back ripped open, both weapons failing, and one hand blown off, still gets up to continue fighting when Marrow is injured, surging energy from his severed arm and using it like a blade to slice two sentinels in half, before sacrificing himself so the other X-men can escape.
Rouge learns Bushido by absorbing the memories of ninja she and Wolverine are fighting. She proceeds to Dual Wield katanas and completely Curb Stomp a dozen Yakuza assassins.
A very underrated one in "Aces and Eights", but Magneto going Papa Wolf on Senator Kelly after the latter hired Gambit to cripple Genosha (breaking Polaris's heart in the process). You do not. Threaten. His kids.
Magneto: You insect! (hurls Kelly's desk out of the way and pins him against the wall) You dare attack my home? MY FAMILY!?
The kids acting like X-Men during the Savage Lands trip, putting aside their differences to stand up against Dog Logan.
Eyeboy gets extra credit since he managed to mow down call everyone out on their issues while shooting robots.
Toad kicking ass and taking names to save Quentin in issue 33.