Truthfully, it's the third one. Easily the third. A lot of you are probably saying "Oh, it was SOOO boring!!!" but truthfully, I loved it's melodic passing and just how beautiful the whole thing was. It really went in-depth with the psychology of Molly, and the entire film really felt very dream-like and mystical. It's the only Pokemon film, aside from 2000 and the Lucario one, I can watch now and still enjoy like I did as a kid. Plus, the third film had all the characters behave in character and still developing, Delia's role was expanded to the point where we saw a lot about her character, and the action sequences were perhaps the best in any Pokemon movie due to the fact that the heroes really didn't win. It's more interesting to watch the villains win, and when you take a step back and realize that the villain of this movie is a depressed girl, the situation is less black and white and more gray, which is something I love.
Plus, it reminds me of Evangelion, my all-time favorite anime, so...
2000 is amazing too: intense plot with an intense story line that still allows us to gain access into the mindsets of the characters. Melody is a fascinating character, and Misty, my favorite character, is given MASSIVE amounts of development. Plus, the soundtracks to both films are amazingly brilliant. I just wish they released the third movie's OST on CD. For the life of me, I've never found one where they released every instrumental track.
However, the first film lacks any real sense of characterization. The plot's all well and good, simple but gets the film going, but everyone's so OOC and bland it's almost unwatchable. The fourth film suffers from coming after the third film, and it's also pretty bland, as is the fifth movie. It gets good with Jirachi, then goes to the garbage bin with Deoxys...but that's just me.