Kaiba utterly trouncing Pegasus, Toons and all. Payback's a bitch, ain't it, Peggy-boy?
The last blow against Anubis. Faced with a monster with 35000 ATK, Yami quickly deduces what kind of strategy Kaiba had planned to beat him with (using the God Cards), and uses his very last card to activate that strategy in his own favor, returning Obelisk, Slifer and Ra to his side of the field after they had been removed from play, before having them combine for infinite power, finally delivering the last blow. It's so magnificent, the area dome around them starts to crack open to reveal boiling lava around the duelists, before the arena erupts in an explosion.
The Blue-Eye's Shining Dragon's final attack was probably the best scene in the whole movie, using its One-Hit Kill attack.
In an anime mostly based around card games, they finally got some physical fights in when Tristan and Joey battled zombies.