That scene where Arceus emerges from his dimension. The skies darken, ominous music plays and it doesn't take long to realize that humanity is beyond screwed now that he's returned to pass his judgement.
Arceus: "The time has come...prepare for JUSTICE!"
Then, in a display of his power, he utterly lays waste to Michina with a single Judgement attack. The way its animated (something akin to a meteor shower of energy blasts) is glorious.
His one-liner in the Japanese version is even more epic.
Arceus: "Judgement day has come! Humanity, prepare for trial!"
Arceus vs. the Creation Trio, and boy did the trio put up one hell of a fight. Sure, it goes as well as one would expect from trying to fight the Pokemon God, but having the Trio, each of which is a Physical God in their own right, fight Arceus is nothing short of awesome.
Dialga and Palkia pull off a Big Damn Heroes moment when they shield the heroes from Arceus' Judgement. Giratina later does the same thing when Arceus dispatches the duo and tries to incinerate Ash and co.
Arceus quickly establishes himself as arguably the most powerful Pokemon in the entire show. He moves fast enough to dodge almost all of the Creation Trio's attacks and anything that isn't dodged is negated altogether by his Multitype ability. In addition, his attacks are scarily powerful and widely varied, so much that it's pretty obvious that nothing other than the Physical Gods that the Trio are could have withstood them. In total, the Creation Trio landed no hits on him, while he tore them apart in only a few minutes of screentime. When Ash and co. return to the present, they find that Arceus has obliterated the Trio, leaving them too critically injured to even move.
The first time Arceus uses Flamethrower on them, Palkia uses Protect, only for the attack to shred the supposedly-unbreakable Protect like paper.
Dialga withstood a massive beatdown from Arceus and still had enough power to warp the heroes through time twice.
Palkia demonstrates a lot more creativity than before, being the only one to pull up a shield when Arceus uses the super-effecive Blizzard while Dialga and Giratina took the brunt of the attack. It uses its spatial manipulation to great effect, warping space to keep the Alpha Pokemon contained to buy time. Unfortunately, the second time it doesn't work so well...
Special mention must go to Giratina, who pulled an impressive psych out on Arceus by powering up an attack while coming up behind him. Only to teleport at the last second and attack from the side instead.
Ash Ketchum swings down on a protruding post and catches the Jewel of Life between his legs. Assassin's Creed much?
Ahem. Ash Ketchum leaps off of a cliff, falls a good twenty feet, snags a protruding post with one hand, uses the swing to catch the falling Jewel with his lower legs, and then safely drops the Jewel to where Pikachu is waiting below to catch it. Benevolent Architecture exists so Ash Ketchum can play Assassin's Creed in real life.note The wooden post is part of a series that are supposed to be used as stairs, but are several feet apart and lack a hand rail.