If Mew and the Wave-Guiding Hero was on the list, that would be my choice... But since it's not, I vote for Jirachi-Wishmaker(even though the English title sounds a bit... lame). It really had what it takes to be a great Pokémon movie! Great story, character development, Ash didn't take all the credit for himself as he usually does... Butler-san was an awesome antagonist, and Jirachi was so cute! Too bad his Japanese voice actress died not long after the movie premiered... Peace to her soul.
Coming into a close third would be Mewtwo Strikes Back!