Aw man, this is a rather tough decision. I really, really like both Mewtwo Strikes Back and The Power of One, but after the numerous streamings of all the Pokemon movies I've done across the past 2 years, I've grown to love quite a bunch of them. I initially didn't really like the Celebi movie very much, as I felt it was way too cliche, and I wasn't a very big fan of Celebi. I was pretty much forced into streaming it during this year's GT though, and I can say I'm thankful for everyone who voted for the movie. I've grown to love it quite a lot, as I feel like I approached it much more openly, and it was one of the few times I've felt like Pokemon actually threw a curveball, and gave us something completely unexpected. And while it's completely certain that they didn't think of that prior to the launch of the anime waaay back, I feel like it still kinda fits in with how Oak trusted Ash enough to give him such a disobedient Pikachu :p
I also really like the Lucario movie, the Darkrai movie, as well as the Keldeo movie, entirely because Keldeo is voiced by Mic Mignogna, but in all honesty, there isn't really any that I don't like. My favourite however, would probably The Power of One, partly because it was my definite favourite back when I was younger, and I've grown quite fond of the plot, and partly because of BIIIIIIIIRRDS!