Mewtwo
(Mewtwo strikes back)
Lugia & the Legendary bird trio
(Pokémon the movie 2000 centered around these)
Unown and Entei
(Pokémon 3 the movie:Spell of the unown centered around these two)
Suicune
(Played an important role in Pokémon 4Ever)
The Lati twins
(Pokémon Heroes)
Rayquaza
(Had an important role in Destiny Deoxys)
Lucario
(Lucario & the mystery of Mew)
Giratina
(Giratina and the Sky warrior)
Zoroark
(Zoroark master of illusions)
Reshiram and Zekrom
(Pokémon Black and White movies)
Kyurem, Virizion, Terrakion, and Cobalion
(Kyurem vs. the swords of justice)
Yveltal
(Diancie and the cocoon of destruction-Yveltal is the cocoon)
Pikachu
(Detective Pikachu)
Source and I’ve watched a lot of these
