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Well I haven't seen them all yet but out of the ones I have seen, my favourites are Pokemon 2000, Mewtwo Strikes Back, and Lucario and the Mystery of Mew. :D
Wow thats a tough one, the first 5 were amazing, but Destiny Deoxys really stands out to me. And then Pokemon Heroes comes in 2nd, Pokemon 2000 in 3rd, and Pokemon 4ever in 4th.