Entei's Big Damn Heroes moment at the end. Entei is cool personified, and being voiced by Dan Green doesn't hurt either.
Entei: If you believe in me, there is nothing I cannot do!
The entire fire fight between Charizard and Entei is a crowning moment for both parties. Entei showed the heroes why pissing off a legendary Pokemon is not a good idea, but even though he came out on top, Charizard made him fight hard for it, despite being in a terrain that suited Entei better and Entei not being held back by that pesky "reality" thing, showing how much Charizard has improved over at that valley.
Said Entei was arguably even STRONGER than a NATURAL Entei due to it being an imaginary Pokémon, and thusly not burdened by the limitations of normal Pokémon (as shown by the Pokémon used by Molly's avatars completely and utterly THRASHINGEACH AND EVERY SINGLE POKEMON used by Misty and Brock while they were trying to buy Ash enough time to confront Entei in the first place.) It also had a terrain advantage; throughout the battle, there were spikes erupting from the crystal walls to both provide footholds for Entei to keep up with Charizard's aerial ability, and for further unfairness, said spikes also erupted in precisely the right locations to slow Charizard down, when they weren't outright impaling him. This makes it arguably possible that had this been a straight fight, Charizard would have put up an even better performance.
At one point, Charizard blasts Entei off the tower he happened to be standing on. Between Entei's roar (which had some strong This Cannot Be! vibes) and Molly's Big "NO!", it's implied Charizard would have WON the fight right then and there if Molly hadn't stepped in.
Charizard uses Flamethrower. An absolute inferno completely swallows up the top of the tower.
Let's face it: Charizard vs. Entei is the best 1-on-1 battle in the anime ever.
Charizard's entrance to the Entei fight. Ash is falling to a bloody death and at the last available second is caught by Charizard, who gives his trainer a quick smile then puts on his game face as he prepares to face the Pokémon that completely curbstomped Ash's entire team.
If you watch that little moment as Charizard catches Ash, Charizard performs some AMAZING aerodynamics. Twirling upside-down quickly, catching him and righting himself in a matter of seconds.
Ash does not care if a legendary Pokémon gets on his bad side, no matter how powerful it is. Imaginary!Entei kidnaps Ash's mother under some very flimsy pretenses. His response is to charge after it, ready to beat Entei down with his bare hands, if it came down to it.
Pretty much anything Delia does after she snaps out of her brainwashing is awesome. The woman is softspoken and kind, but when it counts she's pretty brave, you can now see where Ash got his Determinator traits.
The water Pokemon battle between Misty and Molly epitomizes what every water Pokemon battle should be like. Underwater, where the Pokemon are in their element and can move and attack the way they would naturally, accompanied by some of the most awesome music in the film.
It's a small one, but Ash has a rare moment of Awesomeness by Analysis when he figures out how to break through the crystal wall and keep it from resealing long enough to get everyone through.