Ok I got a few here that I have picked up online so there not my choices and Im not saying its right either but I did watch the hole season 1 and the movie in the time line i'm about to say so here we go...Like I said this may be wrong I am unsure either.
Pokemon The First Movie - During and After "Showdown at the Poke Corral"
Pokemin Movie 2000 - After the episode "Mandarin Island Mis-Match"
Pokemon Movie 3 - After "Fowl Play" But Before "A Dairy Tale Ending"
Pokemon 4Ever - After "Kecleon Caper"
Pokemon Heroes - After "Why, Wynaut
Pokemon Movie Special
Mewtwo Returns - After "Ariados, Amgos"
I havent double checked I just copyed this from some people on a forum made back in 2006.
I would like to know the timeline aswell so if anyone else knows anything or if what I said aint right please say your thoughts and opinions.