This was a tough decision for me. Ultimately, I chose "Mew and the Wave Guiding Hero -Lucario," but I liked "The Spell of the Unown" nearly as much AND I got a greater emotional reaction from the latter.
I chose Lucario's movie because even though the main plot was stupid (Ash getting Pikachu back), the subplot was excellent (Lucario's pain and distrust). Lucario is a multidimensional character.
As for the third movie... I adore Molly. When I saw this in the theater, I didn't cry. I SOBBED. I felt SO bad for her. People even told me to shut up XD
I also like the Japanese version of "Mewtwo Strikes Back." That version of Mewtwo was so complex and philosophical, unlike the dub version where he was just some weirdo megalomaniac D:
I like almost all of the movies, with the exception of the 6th and 7th. The 6th was boring and the 7th reminded me of a scifi movie that would be on TV at 3:30 in the morning. The 2nd was pretty boring too, but I tolerate it because the legend was awesome, the Japanese soundtrack was great ("Minna ga Itakara" is my favorite Pocket Monsters song), and Melody was a fascinating character.