Favourite: Mewtwo Strikes Back, The Power of One, Spell of the Unown (first 3 very iconic and verity. First - dark, second - epic adventure with saving the world, and third - more mature and personal story with message), Lucario and the Mystery of Mew (personal adventure with touching story of lonely Pokemon) and Arceus and the Jewel of Life (saving the world across time and space)
Honourable mention: 4Ever (just good movie with interesting final twist), Heroes (beautiful ending of OS age with first important death), Jirachi: Wish Maker, Pokemon Ranger and Temple of the Sea (most adventures movies, with main role for one Ash's companion's. And 9th movie most longest in franchise), Rise of Darkrai, Zoroark: Master of Illusions (movies with most darkest atmospheres), Hoopa and the Clash of Ages (well, this movie just fun), Volcanion and the Mechanical Marvel (good movie with beautiful atmosphere of fairy tale) and I Choose You (nostalgic and touching bending of new alternative story)
Least Favourite: Black — Victini and Reshiram/White — Victini and Zekrom and (even - the worst) Kyurem VS. The Sword of Justice (they like BW have wasted potential, and just fail. And if 14th movie(s) somehow work, 15th just big fail. Dumb, weak, and for nothing. Plus - without Team Rocket! And this is 15th anniversary movie!)
Honourable mentions: Destiny of Deoxys, Girantina and Sky Warrior, and Diancie and Cocoon of Destruction.