SolVanderlyn
Thanos acquires the fully powered Infinity Gauntlet in The Avengers: Infinity War, but loses when all the superheroes team up together to stop him.
SPOILERS FOLLOW, HOWEVER, BECAUSE OF THE ALL-ENCOMPASSING NATURE OF THIS THREAD, YOU MUST STILL MARK THEM.
My vote has to go to Nagato, from Naruto.
Essentially
Not to mention he is one of the most powerful characters in the series, and has possibly the greatest amount of variation in his abilities, including becoming Mega Man:
This was a hard choice to make. Runner-ups:
2. Uchiha Madara from the same series. Loses out to Nagato for being childishly stubborn in his motivations.
3. Enel, from One Piece. He had such an insane amount of control over his particular piece of the world/story arc. He really felt invincible.
4. Shishio from Rurouni Kenshin. There weren't many redeeming qualities to him, but he was effective as a villain because of this. It's not like he's not able to be empathized with, and he has a tragic story, but his personality, motivations, and methods clearly labeled him as a bad guy, and put him squarely in the "magnificent bastard" category. Only he'd been scarred to the point where his magnificence was purely internal. His exterior was simply "badass" by the point we meet him.
5. Arlong, from One Piece. There are actually villains that are more interesting and effective than him, but he was the first big bad to leave a huge impact on the reader/viewer. The payoff from watching his backstory with Nami to
was amazing, and since he did it first it left a huge impression.
My vote has to go to Nagato, from Naruto.

Essentially
the Darth Vader of the Naruto world, Nagato is a tragic hero pushed past what he could handle. He loses everything he ever cared about, and goes insane as a result. His motivations are that of an empathetic villain - they stem from a desire for vindication - but they're so out there and insane that you can't support him, despite being able to feel bad for him. He's the perfect villain because he has just enough "good guy" in him to keep him interesting while still managing to be a villain you want to see brought to justice, and he has a relation with the main protagonist that doesn't feel at all forced or contrived.

This was a hard choice to make. Runner-ups:
2. Uchiha Madara from the same series. Loses out to Nagato for being childishly stubborn in his motivations.

3. Enel, from One Piece. He had such an insane amount of control over his particular piece of the world/story arc. He really felt invincible.
4. Shishio from Rurouni Kenshin. There weren't many redeeming qualities to him, but he was effective as a villain because of this. It's not like he's not able to be empathized with, and he has a tragic story, but his personality, motivations, and methods clearly labeled him as a bad guy, and put him squarely in the "magnificent bastard" category. Only he'd been scarred to the point where his magnificence was purely internal. His exterior was simply "badass" by the point we meet him.
5. Arlong, from One Piece. There are actually villains that are more interesting and effective than him, but he was the first big bad to leave a huge impact on the reader/viewer. The payoff from watching his backstory with Nami to
his beatdown from Luffy