Mine would probably have to be The Power of One.
I love the story to it, and I think it teaches a good lesson.
Also, it was, yet, another introduction to the upcoming "new" Johto Pokemon.
And the score to the movie is fantastic, in my opinion. "Lugia's Song" is gorgeous.
I agree on the music believe it or not my orchestra at my school once played it and it was awesome. I loved the violin part it was so fun to play!
Pokémon 2000: The Power of One. It has great animation, lucid, poignant, and confident music in tones, is epic by nature, allows fruition for great battles, had good characterizations and is moving in the support of the characters, and just feels like one solidified movie to me (in villainy it might be a tad inept but I think Lawrence III is less the villain, but rather an ephemeral hindrance... I chalk the villain up to the natural disasters impending along the horizon in this film). I intensely, intensely love Lucario and the Mystery of Mew, Heroes, Destiny Deoxys, and the Mewtwo Returns special (if that counts), but Pokémon 2000 just has sheer awesomeness for me.
Easily the first one, the worst one was with Manaphy. I wanted to kill that thing, it was annoying and it was too sappy for it's own good.
I've only seen 2000 and the first movie. So I'm going with the first movie.. Wait.. The last time I saw 2000 was in 2001..This be confusing. O_o I need to watch more movies.