There are two in Wolverine's introduction scenes. The first comes when he is in the cage, not really fighting, and then breaks his opponent's hand by punching it. Awesome because it properly confirmed (for those who missed the blindingly obvious fact that this was Wolverine) exactly who it was. The second occurs when said opponent confronts him later, threatening him with the fact he know's he's a mutant and attacking him with an knife. The look on his face when he realised that Wolvie isn't just Made of Iron, but has foot long metal claws as well is utterly priceless.
They also work in Wolverine's signature CMOA from the comics, where he unleashes the two outer blades around someone's throat and threatens to pop the middle one. When the bartender threatens him with a shotgun Logan uses his other hand to claw it clean in half, before calmly walking away.
Magneto: "You homo sapiens and your guns."
Toad gets a wonderful moment in the first movie when he utterly trounces Cyclops, Storm and Jean without even breaking a sweat. Adaptational Badass, thy name is Mortimer Toynbee. Leave it to Storm to screw it all up...
Storm's moment was pretty cool though.
Mystique revealing herself out of focus then proceeding to kick Senator Kelly's arse or pretty much any time Mystique is on screen
Cyclops dispatching Sabertooth and Magneto, while also coming up with a plan that uses every X-Man's power too their advantage is really awesome to this trooper, as Cyke was often shafted in this series.