The anime medium consists of a wide range of viewing options, but a large fraction of its storylines follow the standard hero's journey trope — one that necessarily ends (and perhaps even begins) with the villain. In fact, major narrative conflicts are often resolved when the protagonist actively takes up arms against the antagonist.
As such, anime villains can be considered the keystones of their respective stories, explaining why so many of them possess power beyond the hero's wildest imagination (at least until the end.) While a few are strong enough to level city blocks, while others are capable of destroying entire galaxies.
All For One — My Hero Academia
All For One appears as All Might's counterpart and nemesis, refusing to make a live anime appearance until he recuperates from his last battle. When he does though, he effortlessly takes down a number of Pro Heroes, such as the phenomenal Best Jeanist, and forces All Might to wring out every last drop remaining in One For All.
All For One is defeated by the United States of Smash, but he continues to manipulate the situation from his cell in the inescapable prison fortress of Tartarus.
Ragyo Kiryuin — Kill La Kill
Ragyo Kiryuin reveals the protagonist, Ryuko Matoi, to be her long-lost daughter, but this just makes the latter more eager to take the villain out. Unfortunately, the combined efforts of Ryuko and Satsuki Kiryuin pale in comparison to their mother's utterly captivating martial artistry.
Given that Kill la Kill is a parody of the shonen genre, it's not surprising that Ragyo's final outfit, Shinra Koketsu, literally transforms her into a gigantic being floating in outer space.
Shinobu Sensui — Yu Yu Hakusho
Yusuke Urameshi spends hundreds of hours training and enhancing the offensive force of his Spirit Gun just to defeat Younger Toguro at the Dark Tournament.
He succeeds in the end but is immediately thrown into a new arc with a far more fearsome antagonist, Shinobu Sensui, whose Sacred Energy completely eclipses the Spirit Gun. Even Kuwabara, Hiei, and Kurama fighting at full strength can't defeat Sensui, nor can the newly activated Mazoku Yusuke.
Eren Yeager — Attack On Titan
Eren Yeager starts his journey as a traumatized child, swearing what sounds like an empty oath of vengeance against the Titans (mainly on behalf of his dead mother, Carla.) Grisha, his dad, secretly imbues him with two of the Nine Titans — the Attack Titan and the Founding Titan, but Eren only uses the first until the end of the manga, which is when he transforms from protagonist to potential antagonist.
He somehow convinces Ymir Fritz to unleash the complete power hidden within the Founding Titan, which converts him into the largest entity ever seen in Attack on Titan. Eren's size notwithstanding, he also has the authority to temporarily "reincarnate" all the past s of the Nine Titans to do battle for him.
Father — Fullmetal Alchemist: Brotherhood
Created in Xerxes as the Dwarf in the Flask: Homunculus, Father tricks Van Hohenheim into practically killing the 1 million inhabitants of the kingdom, thereby using their souls to grant himself and his "partner" near-eternal life and the gift of alchemy without consequence.
Father's powers are vastly augmented once he absorbs the entity known as "God" or "Truth," allowing him access to telekinesis at the molecular level. It's only thanks to Hohenheim's centuries worth of efforts in creating the Umbral Circle that Father is reverted to his usual form.
Meruem — Hunter X Hunter
The Chimera Ant King is born with incalculable reserves of life aura because his mother consumes thousands of Nen-aura during his gestation. He is immediately able to display his talents at Gyo, Ko, and Ren, which take most proficient Hunters months or years to master.
Although Meruem's battle with Netero technically kills him (via a complicated subterfuge involving poisoned nukes), his initial strength is exponentially magnified after two of his Royal Guards, Youpi and Pouf, "feed" the king parts of their own bodies.
Boros — One-Punch Man
As the chief of the Dark Matter Thieves, Boros exhibits a level of power that is yet to be sured by any other villain in One-Punch Man. Saitama faces no barriers when fighting him, though, and doesn't use his full strength to annihilate Boros.
That being said, the fact that he suffers several direct attacks from Saitama without imploding is evidence of his might. Boros's Hosei Hokoho is enough to literally peel the crust off the Earth, so it's fortunate that Saitama limits the damage to the planet's stratosphere.
Kaguya Otsutsuki — Naruto
Kaguya Otsutsuki is divine in many ways, if not in of her actions. She can fly, fuse with her surroundings, absorb Chakras, travel across dimensions, perform masterful psionic feats, heal from significant damage, and also transform her own skeleton into the terrifying All-Killing Ash Bones technique.
Then there is the Expansive Truth-Seeking Ball, which is generated through the God Tree. Vanquishing Kaguya takes an inordinate amount of effort, skill, and luck.
Yhwach — Bleach
Bleach's Yhwach is more powerful than every character in the series, long before he even reaches Soul King level. He doesn't need more than a single reishi sword-arrow to kill Yamamoto Genryusai, a man whose bankai is so dangerous that it could vaporize Soul Society.
After the Soul King is absorbed into his physiology, Yhwach becomes nigh-invincible, forcing the heroes to think up alternative strategies that don't revolve around brute force. Yhwach is ultimately defeated (?) by Ichigo Kurosaki after the former's immortality is inactivated by Uryu's Still Silver arrow.
Beerus — Dragon Ball Super
The God of Destruction is no weakling, thanks to his exceedingly potent Energy of Destruction. If this isn't enough, he can also go into his Fury state, where the energy encapsulates him like a shroud. Beerus's durability is as complete as his offensive and defensive moves, and he's shown himself capable of wiping out half a world by simply tapping his fingernail.
Beerus may be weaker than Whis, his Guide Angel Attendant, but he apparently possesses so much power that he could, in theory, eradicate Universe 7.