Awww man, this is a hard question to answer because I can't ignore the nostalgia factor XD
2.The Power of One was incredible with Lugia and Lugia's song in it XD and don't forget about Donna Summer's Power of One song!
3.Spell of the Unown is special to me because that's probably the only time Unown will ever show such devastating power in the franchise. I liked it also because of the relationship Molly has with Entei, and that we get to see Delia as an important character.
4.After watching Voice of the Forest, Suicune was my favorite Pokemon. This movie introduces a beautiful forest and a very special character named Sammy Oak through Celebi, a time traveler.
5.Pokemon Heroes really sticks out to me because this movie is why I want to go to Venice so badly. Alto Mare is amazing, especially when you have dragons as guardians XD
6.Jirachi Wish Maker was a dramatic adventure where we get to guide Jirachi back home to Forina, and away from an evil Magician/Scientist named Butler. This movie has some amazing action scenes where we get to see people riding dragons to defeat a kaiju lol. Make a Wish is a beautiful song from this movie, everyone should listen to it XD
8. Lucario and the Mystery of Mew is really interesting because it has historic events affecting the present, new pokemon like lucario and weavile, legendary golems and the return of an old friend, Mew. Lucario's journey to find to truth of his master Sir Aaron is action packed and heartwarming. The ending song, We Will Meet Again is really good too.
10. The Rise of Darkrai has an awesome Dark Knight as the main character, and has the best title logo of all. Gods of time and space pose a threat against our protagonists and its up to a nightmare Pokemon and some kids to play Oracion and stop a dimensional rift.
11. Giratina and the Sky Warrior was beautiful with its fjords and landscapes. The Japanese ending song ONE, is really cool as well as the English ending, This is a Beautiful World.
12. Arceus and the Jewel of Life is where we get to see the powers of the universe's creator. (Which wasn't that powerful, but it was nice to watch
I don't have much to comment on the rest because they were only a little mediocre compared to these I mentioned, or because gen 5 and 6 made relatively bad impressions when in came to the movies.
But we can't forget the very First Movie, can we?
Surprisingly, this movie doesn't have much nostalgia value to me, mostly because I was too young when I watched it.
However, even when I'm older, I still think this was a great movie. It had a really dark backstory to it, which none of the future movies ever had, and conveyed a good message. Mewtwo's quote will never be forgotten.
"I see now that the circumstances of one's birth is irrelevant. It is what you do with the gift of life that determines who you are."
(Sorry about all the fanboying XD)