The memorable opening scene where Jack, disguised as one of the bad guys, seconds before his reveal "swabbing the deck" - steals Manaphy's egg and makes an escape a la James Bond.
The nothing-short-of-epic climax—particularly the entire run-for-your-life sequence where Ash gets to escape a ruins that's rapidly flooding with water and then going to set things right with the crystals...under SEA water, in a big room deep beneath the ocean, running out of breath at the last second, and then (admittedly with a little help) going on to save the day... and then the movie-winning power-up. ALL WITHOUT HIS TEAM.
An understated moment: While Ash is putting the crystal into place, he flips his hat back for the first time since the original series.
Kyogre, when it participated in the final battle along with all the other water-type Pokemon. Particularly it's Hyper Beam which, taking a page out of Lugia's example, pretty much wrecked the ship with a single shot.
Special props to the soundtrack, especially the track "As Long As I Can Hold My Breath" for being a noteworthy piece of epic music.