Haha, I had this problem. If you start watching a movie, almost every one of them has a scene right at the start that shows ash and friends and all their pokemon... you can then tell where it fits in. Ie take note of which pokemon are at which evolution etc then keep watching episodes till they match.
This is what I know so far.... I'm up to series 10, as I progress I will post the rest.
The first 6, I got from this thread:
https://www.pokecommunity.com/showthread.php?t=189941
Mewtwo Strikes Back - After "Showdown at the Poke Corral"
The Power of One - After "Mandarin Island Mis-Match"
Spell of the Unown - After "Fowl Play"
Celebi: Voice of the Forest - After "Kecleon Caper"
Mewtwo Returns - After "Ariados, Amigos"
Heroes: Latio and Latias - After "Why, Wynaut?"
These, I worked out on my own:
Jirachi Wish Maker - After "Seeing is Believing" (because May has Beautifly)
Destiny Deoxys - After "A Shroomish Skirmish" (because May has Combuskin)
Lucario and the Mystery of Mew - After "The Right Place and the Right Mime" (because May has Squirtle)
The Mastermind of Mirage Pokemon - After "Pokémon Ranger! Deoxys Crisis! (Part Two)" (because Pikachu had already mastered Bolt Tackle, and later when it was aired for a second time, this is where it was placed).
Pokémon Ranger and the Temple of the Sea - After "Aipom and the Circumstance" (because Ash has Aipom and Aipom respects him)
