Both battles between Rayquaza and Deoxys are awesome.
And all of Deoxys's transformations are epic.
Rayquaza shows the true power of a legendary Pokémon, taking on the titular Pokémon in the North Pole (Rayquaza's biggest weakness is Ice), and proceeding to blast off chunks of its body with Hyper Beams. Rayquaza is thrown in the icy waters, and, when Deoxys approaches the spot, it emerges with a fully charged Hyper Beam, that is unleashed at point blank range on Deoxys' (rather terrified) face, and proceeds to blast its body to smitheerens. It got better...
When Rayquaza blasts through Deoxys's force field and proceeds to continue the battle with Deoxys.
The scene where everyone helps in bringing back the power, which also includes the help of Pokemon.