Wolverine getting his adamantium skeleton and claws, while cool in itself, is nothing compared to the following scene of him overhearing Stryker's plan to erase his memory, and proceeding to burst out of the water roaring in rage, claws extended, and his extremely toned muscles articulated by the dramatic lighting, scaring the crap out of everyone else present.
Another one: after reeling back from Zero's quick headshot, he just turns back showing the uselessness of bullet against adamantium, once that happen you know asskicking is going to happen, Zero's Oh, Crap face says it all.
Wolverine killing a helicopter with his claws. And then killing Zero by walking away and letting his claws spark against gravel, thus igniting the leaked fuel... Cue Unflinching Walk. Just plain beautiful.
He also gets one later on when fighting Sabretooth after being reinforced with adamantium, owning him beautifully and mocking him while he does so.
Wolverine and Sabertooth teaming up in the final battles.
Sabretooth gets one when he's taking a beating from teleporting mutant John Wraith (which is a CMOA for Wraith). Sabretooth smiles and says "You know, John, there's something I always wanted to tell you..." Then he reaches out to where he knows Wraith will be next, grabs him by the spinal column as he materializes, and finishes with "You're predictable." Spine-breaking ensues.
Wade Wilson gets his own CMoA scene. The future "Merc with a Mouth" walks into a room full of armed Mooks, swords spinning to block bullets from either side, and proceeds to whoop ass. The best moment has to be when he sees that a mook is about to take a shot at him (via a reflection on one of his sword), spins around as the shot is fired, and cuts the bullet in half. The two halves end up killing two mooks behind him.