Ygdrassil from Tales of Symphonia, a perfect balance of an imposing, poweful character with fleshed out tragedy and sympathetic backstory and a fantastic parallel to Lloyd the main hero.
Magolor from Kirby's Return to Dreamland was really memorable in execution, from both story and gameplay, also the Hyness + Void Termina combo in Star Allies, Hyness just for his insane personality that only gets more tragic the more you uncover of his past and Void Termina marks Kirby's finest moment, for both its origin and entire build up of decades of the series.
Kefka is really good.
Bowser in Odyssey and Dream Team is amazingly satisfying to fight, his character and plans are very well done in these games. Dimentio from Super Paper Mario and Princess Shroob from Partners in Time are great as well.
Vergil in Devil May Cry 3 is absolutely legendary, as a rival in an action title and from the whole story development.
