Antagonists

Pokemon:
Mewtwo: Yes (many clones)
Legendary: Yes

Ranma 1/2:
Saffron Phoenix: No
Kirin: Yes
Toma: Yes

Accel World:
Black Vice: No
Nomi/Dusk Taker: No

Sailor Moon:
Queen Beryl: Yes
Doom Phantom: No
Death Busters: No
Black Circus: No
Sailor Galaxia: No

BlazBlue:
Nine: Yes
Terumi: Yes
Hazama: Yes
Susanoo: Yes
Relius Clover: ?
Arakune: ?
Azrael: ?

RWBY:
Cinder: No
Salem: No
Neo: Yes

Slayers:
Val Garv: No
Hell master Fabreizo: No

Code Geass:
King Charles: Yes
Marianne: ?
V.V.: ?

Yu-Gi-Oh:
Zork: No
Yami Bakura: No

Yu Yu Hakusho:
Togoro Brothers: Yes

Inuyasha:
Naraku: Yes
Kagura: Yes
Kanna: Yes
Byakuya: Yes

Kingdom Hearts:
Vanitas: ?
Dark Aqua: ?
Maleficent: Yes

Fate:
Gilgamesh: Yes
Kotamine Yes
Angra Mayu: No

Soul Eater:
Medusa Gorgon: No
Archane Gorgon: No

P4/P5:
Shadows of P-cast: Yes

Cannon Fodder

Mew Two Pokemon clones?
Ranma 1/2 Ghosts
Accel World: NPC monsters (enemies)
RWBY: the grim
Slayers: Monsters/Bandits
XXXHolic: Ghosts
Demon Slayer: Demons (vampires)
Yu Yu Hakusho: Demons/apparitions
Inuyasha: Demons(monsters)
Kamen Rider: Mutants
Kamen Rider Ryuki: Mirror Monsters
Kingdom Hearts: Heartless and Unversed
Fate: Solomon Demons
Tsukihime: Vampires
Blood+: Chiropterans
Persona: Shadows (manifestations of peoples psyches)
Evil Dead: Deadites
Guyver: Zoanoids
Sailor Moon: Monsters from four seasons