The first movie was probably my favorite also, although the careless errors made in the dub did kind of get annoying, but it was still the best imo.
My second favorite was probably Pokemon2000, I'd say it was the most "actiony" one besides the first movie.
Then Spell of the Unown. I thought that one was adorable. The battle with charizard and entei was a bit too long, but I still liked it.
Pokemon4ever, Jirachi Wishmaker, and Lucario and the Mystery of Mew are next.
I found the plot to Heroes, Destiny Deoxys, Pokemon Ranger and Prince of the Sea to be lacking in interesting concepts.