Pokémon possessed by artifacts linked to various Legendary Pokémon. In this possessed state, not only are they embued with additional power, but they are also able to be guided by the Pokémon who is related to the artifact.
Legendary Pokémon turned primal and feral by some form of imbalance in the forces they govern, they are brutal and incredibly bloodthirsty, relying on battling survival instincts long-since extinguished from even the darkest of Shadow Pokémon's heart.
Pokémon turned into fighting machines by artificially sealing their hearts shut through mistreatment, abuse and intensive training. They are known for attacking even once their prey is unconscious, and will even assault humans. The training can be undone with love, patience and care, and so ready the Pokémon for a purification procedure to banish the last of the darkness clinging to them.
XD Shadow Series
Pokémon whose hearts were shut artificially so well that there are very few hopes of them ever recovering from the shadow Pokémon procedure. Purification never works on them, and their inner darkness has even corrupted their outward appearance, turning them much more menacing.
Pokémon created by nightmares, warped into strange shadows of themselves. Although their appearance is warped and their attacks can be different from the usual, they still behave as their normal counterparts would.
Pokémon who were born or evolved in high-magnetism areas, causing peculiar mutations. Affected Pokémon receive slight coloration and anatomy changes, as well as having types different from their normal counterparts. Delta Pokémon are also known for certain evolutionary quirks, such as reacting only to the radiations of a Mist Stone.
Pokémon that have been infected by the previously unknown mutation of Deoxys, Ribon. In the early stages of infection, the Pokémon only display a slight "glazed" sheen, and become lethargic. Once completely infected, the affected Pokémon no longer eats, sleeps, or breathes, and their entire body, organs and bones included, have merged together into flexible colored "glass". It should be noted that once infection sets root, the Pokémon is no longer able to evolve or breed.