Had to think on this for a while, and in the end instead of some childhood favourites I've picked a recent one, Emet-Selch from Final Fantasy XIV.
Long story short he has an amazing character arch and is one of those epic villains who you love to hate and hate to love, who you can't help it but feel sorry for and understand him.
Spoiler warning, if you haven't completed Shadowbringers yet, you might want to skip my explanation why I think he's amazing.
Emet-Selch is the main antagonist the Warrior of Light (the player) has to face in Final Fantasy XIV's Shadowbringers expansion. He's an Ascian like the enemies we have faced before, but he's one of the few, who remembers the world as it was before it got split into 14 shards. Even though we know he is our enemy and he doesn't try to deny it either, he decides to join us on our adventure as an observer, and for a while even helps us from time to time... until at one point he reveals his plan and turns on us.
Through his tales we learn a lot about the history of the world and he also tells us why the Ascians are trying to rejoin the 14 shards, and make the world whole again.... even if it means destroying life on it as we know it.
His character arc and story takes us on such an emotional rollercoaster, as we doubt him, hate him for what he's done to one of our comrades, for what he wants to do to us.... yet when we walk through the illusion city he has built to remember the old world, realisation hits that he has lost everything and would do anything to see his loved ones again... and wouldn't we all do the same?
And even after we defeat him, he will appear a few more times and help us unexpectedly... and we have to get to the final chapters of the next expansion, Endwalker to understand why did he change his mind and deem us worthy to trust us with the remnants of his world.
There were a few scenes in this game which made me cry, I didn't expect his final words to be one of those scenes....
"Remember us. Remember that we once lived."