In The Bridge (MLP), the Nexuses of Magic are this in spades, the God of Extinction from Terra, Bagan, and Nexus of Light Magic, Harmony. Both are described as gods and are the only known beings who could fight the other one on one. It's noted even Grand King Ghidorah, one of the strongest kaiju in existence, fighting either of them alone would be suicide. Grogar, the Nexus of Dark Magic, is stated to be on the same tier as Harmony could only just barely defeat him.
Chains of Reality has both versions of the Loud family: More specifically, the original prototype sisters, the new set of sisters from the new reality, and Lincoln/Proto-Lincoln/Sincoln. Interestingly enough, however, while all of them have access to divine powers and such, only the prototype sisters and Proto-Lincoln/Sincoln have an innate knowledge on how to use them, while Lincoln and the Neo-Sisters have to be trained in order to access them.
Thor, Loki, Odin and Frigga, for instance. In fact, Royal Asgardians in general, and ordinary Asgardians with specific mantles of power, e.g. Heimdall and Sif.
Harry, needless to say, is progressing towards this point thanks to his ancestry. Since his maternal second cousin is Jean Grey and he got the same X-Gene, he gets it twice over, though in terms of raw psychic power he's still well below Jean and Maddie. By the sequel, he's on the borderline of this and Person of Mass Destruction.
The Hulk qualifies as this, being the only person bar Odin capable of restraining Thor in full berserker mode.
Of the Avengers' off-screen previous enemies, Count Nefaria qualifies, as does the Juggernaut, who appears in the sequel, fighting evenly with Thor. Then he made Thor mad. Cue Unstoppable Rage.
Gravemoss, technically. Like the Enchantress in the comics, he's pretty weak in the higher realms, like Asgard, but on Earth, he's an incredibly fast killing machine who can rip through concrete with his bare hands.
Wanda and Doctor Strange arguably reach this level, with Wanda capable of dropping meteors on people's heads with pin point precision and Doctor Strange challenging the entire White Council to a duel. That's a couple of thousand Persons of Mass Destruction, a few of whom reach the edge of this weight class. And they backed down. While a lot of this is his reputation, and the sequel indicates that his natural power level is Person of Mass Destruction level and that he's actually weaker than Wanda, his sheer precision and creativity mean that he approaches this level — he's the Sorcerer Supreme, and fights and/or manipulates Eldritch Abominations for a living. And if he needs more power, he can get it — this is the man who steals the Tesseract from Asgardian maximum security when he's bored. Essentially, he and Wanda are both in between Person of Mass Destruction and Physical God status, but Stephen is a few steps below Wanda.
Omega Class mutants, though rare, fit this criteria — the above mentioned Wanda, her father Magneto and eventually, Jean Grey and Maddie Pryor.
Alan Scott as the Green Lantern, who is mentioned as having been SHIELD's countermeasure against Magneto (though without the ring, he was "only" a Badass Normal). When the full potential power of the Lantern is revealed in Unfinished Business, it's stated to be the sort of power that creates pantheons - and it lives up to the billing.
Dracula, King of the Grey Court, who barely lost a fight to Thor centuries ago, then promptly hunted down and killed another Physical God, Perun, the Slavic God of Thunder, just to prove he hadn't gone soft. He demonstrates his power by swatting Voldemort like a bug, and beating Harry to a pulp twice, the first time while simultaneously reflecting a psychic attack from a Cerebro-amped Charles Xavier.
Merlin is later confirmed to be on this level, with Strange himself stating that as far as magical practitioners go, "Merlin was and remains on another level entirely."
Nimue, after she takes control of the full power of Project Pegasus, turning her into a Dark Lantern. Given that she's an ancient and seriously powerful Person of Mass Destruction to begin with, this is... alarming.
The Equestrian Alicorn Princesses are confirmed as such; while they're implied to be younger than the Alicorns still living in the outside world, they're incredibly powerful, and much more capable in canon. Celestia flash-fried a Kraken attacking Manehattan as soon the opportunity presented itself; and Cadence was able to beat up Fik'iri despite the latter being older than her, since Fik'iri is now her equal in power following her loss and de-powering in the "Abyssinian Divine Coup" event.
Golden Scepter, a surviving antediluvian Alicorn Emperor from the Alicorn Civilization, is an "Antecedent"-type god, meaning that he's extremely ancient, and extremely powerful compared to the newly-Ascended Alicorns of current generations, including his nineteen sons, who are Alicorn demigods. As the Alicorn god of Psionics, he's one of the strongest psychics on Equus, to the point where his entry mentions that even the mightiest Alicorns couldn't hope to match his potent mind. Even one of his mortal Pony generals, General Aurum Lupus, had to rely on divine empowerment to even confront him during the "Aurum Apostasy" conflict after he turned traitor. As such, any attempt to fight him will almost always result in an extremely one-sided Curb-Stomp Battle. However, it's stated in his own entry that he often takes the form of a rather normal-looking Alicorn when among mortals, and whenever he needs to go unnoticed, he appears as an unassuming Earth pony stallion named Revelation. Like Queen Mzazi and Isati, he's a benevolent Humanoid Abomination who is much more powerful in his true form.
Blue Suede Heartstrings is one due to being an Alicorn. It's stated that he has an extremely impressive mastery over music in general, given his origins as a famous musician, and after becoming the god of Music, he's very skilled and creative with it. His domain of Humility gives him telepathy, empathy, and precognition, and his domain of Performance gives him shapeshifting abilities and enhanced combat skills thanks to his domain of Performance. Lastly, he is a Love deity who embodies Philia Love, allowing him to see the bonds of friendship that tie mortals and/or divines together. Due to his humble character, though, he often takes the form of a mortal, though it's implied that his mortal forms are no slouches, either. His entry notes that he is a "prodigy" deity, which gives him an accelerated rate of physical and magical growth compared to normal deities, and is already showing signs of growing a second pair of wings. And because he was born in the early Second Age, he's ancient enough for people to start making guesses as to what his origins story is.
Bossa Nova Heartstrings, Blue's older twin brother is one due to being an Alicorn. While he isn't a "prodigy deity" like Blue is, being a Death god automatically makes him powerful, as he can summon weapons out of thin air, appear in multiple places at once, and has power over spirits of the deceased, including the power to free them from whatever is binding them to the mortal planes. His Death domain also gives him both clairvoyance to sense when people are going to die, and psychic foresight to predict how people are going to die. His Music domain gives him control over both Magic Music and sound magic, and he has almost all the same abilities as Blue, who taught him how to use said abilities. His domain of Joy also gives him telepathic and empathic abilities that allow him to detect and spread joy, especially among the dying and deceased. As Blue's older twin brother, Bossa Nova is also pretty ancient and is only marginally older than him, though being a Death god who started out as a stillborn foal means that he doesn't have to deal with people constantly guessing his past like Blue does.
As an "Antecedent"-ranked Zebra goddess, Queen Mzazi is one. As a goddess of Alchemy, she's one of the most powerful alchemists and potion-makers on Equus (and has mentored younger deities who share her domain or partake in the craft). She can generate lightning potent enough to electrocute Giants and Dragons if she chooses, and has created cataclysmic lightning storms for both offense and protection (one imperialistic fleet was wiped out down to its last soldier for trying to invade Zebrica, and Zebrica itself is surrounded by a storm whenever she goes traveling). This comes from being a goddess of Nature, though Kendell2 has stated that she embodies the stormy aspects of it rather than plant manipulation as Nature-based deities usually have. And due to being extremely ancient, her divine strength is proportionate to her "age" and she is incredibly well-versed in magic in general. As a hallmark of her "age", her true form as a Zebralicorn goddess is a gigantic Humanoid Abomination with a mane and tail composed of lightning storms, wing feathers made of lightning, and a magical wing gradient going from pink to mint-green.
Prince Healing Song is one, due to being an Alicorn god from the Second Age. Like Blue Suede Heartstrings, his mentor, Healing Song has an incredible mastery over music, which manifested as the Music domain when he Ascended to godhood. Unlike Blue, though, he is skilled in using its healing/empowering aspects and mostly chooses to do that over using music to attack people. His Potential domain gives Healing Song potent precognitive abilities and the ability to empower allies with their future potential, and his Teaching domain gives Healing Song a psychic intuition that allows him to adapt to his students' needs and learning developments. His Psionics domain gives him great psychic abilities like telepathy and psionic telekinesis, and coming under the tutelage of Emperor Golden Scepter and his son, Prince Crimson Star, has given Healing Song new psychic abilities and made him even more powerful. Being a "prodigy deity" also makes him stronger compared to "normal" deities in overall power and growth. However, because of his pacifistic beliefs, Healing Song mostly chooses to serve a healing/support role and only uses his offensive abilities when necessary, though this has prevented him from fighting effectively at times.
As an Alicorn, Prince Sparkling Wing is one, despite being one of the younger members of the Church. Notably, he is skilled with weather magic, a powerful empath, and can empower mortals and forge temporary bonds that allow them to share each other's abilities based on how deep they trust each other.
A Crown of Stars: Daniel and Rayana are the Immortal Rulers of Avalon (Big Good of the story, but not the heroes). Having Ascended to godhood long ago, they always wear a humanoid shape and they are immortal, very ancient, can manipulate souls and travel through time, space and dimensions, have some level of reality-warping and omniscience, and Rayana's speciality is magic. They also are pretty cool "people".
Dimensions: Takato and Rika, thanks to being the current incarnations of Chaos and Harmony respectively. Also a major case of subverted Personality Powers.
Getting Too Old For This: Harry Potter is far more than just a powerful wizard; he's the "Master of Death and all that entails." Not only is he unkillable (or rather, he'll simply get better), Harry is also responsible for the deaths of all things. An example is when he stopped the Hogwarts Express from being scrapped. His intervention, preventing the "death" of the last steam engine on Earth, caused a massive resurgence in interest in steam power across the galaxy, such as the Asari creating a steam powered spaceship. Liara T'soni describes him as "the next best thing to omnipotent while being as far from omniscient as everyone else."
Harry Potter: Death comes for everything. People die, yes, but ideas also die. Cells die, sanity dies, seconds die and in the end all answer to me. An accident preventing one such death resonated across billions of cubic light-years.
The God Squad is built around this idea. Celestia, Luna, Discord, Chrysalis, Tydal, and Cadence are all literal gods who are forced to keep almost all their power in check, lest they destroy the universe. Their normal bodies (which are nearly impossible to hurt and filled with more power than any mortal in the world) are merely 1%. At 10% we get Nightmare Moon territory, at 15% we have Discord, and Tydal has managed to go to 40% (turning him into a cross between a Kaiju and a weapon of mass destruction). Celestia has stated that their true forms are so large the planet would be a grain of dust to them.
In the first arc, the Legion of Super-Heroes turn to the Greek deities to save Supergirl's life. They meet Zeus, Mercury, Venus, Vulcan and Apollo, and it's mentioned that the other Olympians are "on a day trip to Asgard".
In the third arc, Destruction of the Endless, the anthropomorphic personification of the self-named cosmic principle allies himself with the heroes.
HERZ: Rei. Her soul was Lilith's, an Eldritch Abomination was the mother of all life on Earth. However her body was Shinji's mother cloned body. In the battle of 2015 she absorbed Adam and her bigger body, becoming even more powerful, but she kept her mortal form to live with her family for a while longer.
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH has Harry Potter. He can see subatomic particles by squinting, seemingly teleports across galaxies, and has destroyed entire planets for no reason at all.
I Am What I Am: Willow fulfills this to the point of actually being considered a god by several religions. Xander explains that while normally only people with almost no magical ability can forge magical weapons, Willow manages it by turning magic into solid weapons rather than forging metal into a magical weapon. Xander once asked how long she could keep up an enhancement spell that (after years of training) he can hold for roughly four seconds. Willow, after asking the date, tells him she's been maintaining it for eight years.
Princesses Celestia and Luna, of course, as per canon, but the story also adds their equally strong brother Prince Empyrean, and their even more powerful parents King Titan and Queen Terra. And then, near the end of the story, Twilight taps into the full power of the Elements of Harmony and becomes so powerful that only Titan himself is able beat her in a fight. And then, during the climax, she absorbs the powers of Harmony and becomes an alicorn who is Titan's equal.
Of all ponies, Fluttershy becomes one during the Battle of the Everfree. And she does so in epic fashion — she uses something equal to the Royal Canterlot Voice to browbeat the most ancient of all dragons into switching sides, then rides him as her personal steed in the story's most impressive Big Damn Heroes moment.
The Infinite Loops: Most loopers past a certain threshold probably qualify, but the trophy has to go to the original seven. They've been looping for so long that they're all literally older than time in any given iteration of the universe, (Ichigo said that he once stuck around until the entire universe burned out), and Ranma in particular, being the oldest, is so powerful that he can collect Death Stars. Any one of them could ascend to true godhood by flexing, if the urge struck them, and they're generally regarded as the most powerful beings in the multiverse.
The Infinity League has Miranda Eon, the human-looking incarnation of an Eon God.
The Keys Stand Alone: The Soft World: The Pyar gods physically inhabit the substance of the White Tower, which is keeping them alive.
The Legend of Link: Lucky Number 13: Most characters are physical gods, including Link himself after The Reveal. Fate and Destiny are thought by "regular" gods to be Powers That Be, fundamental to the structure of reality, but their deaths at Link's hands prove the only real difference is that they are older and stronger; reality itself carries on just fine without them.
The Moonstone Cup: There's a small number of very ancient, very powerful beings who rule over nations of regular mortals and view themselves as deities with little hyperbole. In addition to Celestia and Luna, these include their "cousin" Najstariot, the dragon queen, and the huge wolf Amarok, who rules over lesser wolves and commands the magic and spirits of the cold north.
Myths and Birthrights: Every single alicorn. They're even called (and treated like) gods.
Nobody Dies: The more powerful Angels are considered this, even by the other Angels. ADAM in particular is in a class of his own, with literally world-shattering power. Observe Israfel's description of Zeruel, second only to ADAM in power: Imagine a being with a heartbeat that could move an island. A gaze that can burn down a mountain. More power in his little pinky then we have in our full, entire form. Imagine something that early Lilim wrote about, thinking it was Omnipotent, Almighty, and a vengeful God. Imagine that, and maybe you can imagine Zeruel.
The Non-Bronyverse: Celestia and Luna are explicitly mentioned to be gods. TD accidentally gets in on the act in the AU story TD the Alicorn Princess.
On a Pale Horse: Harry Potter (or at least a version of him) has become the embodiment of Death itself, is so powerful that curiously tugging on the magic attempting to summon him causes the entire building said summoners are in the jerk, and is old enough that he uses the Earth's age as a unit of measure (at one point he notes he hasn't been a hero in about "four Earth's worth of time").
Origins: Sarah possesses telekinesis, teleportation, mind-reading, and a massive Healing Factor, mostly because she possesses all Siren powers combined with the Force. Considering who created her this makes perfect sense.
All of the Alicorns and Draconnequi qualify, except their Elders, who are actual gods. It's said that Celestia, when not holding back, could destroy an entire planet with a solar flare if she so desired, which thankfully she doesn't.
There's also Queen Tiamat, the Mother of All Dragons and their patron deity. Her power alone qualifies her for this, as she single-handedly turned the tide of the Dragon-Hooviet War when she entered the fray. By the time she was finished, half the Hooviet Empire was blazing ruin with her willingly stopping just short of the capital. The Hooviets didn't leave a scratch on her. Her husband Bahamut is every bit as strong.
Mother Deer is to her people what Tiamat is to the dragons, though she's also a pacifist, so she leaves the fighting to her followers.
In PropagationTaylor, as Eden Reborn, is a very, very close equivalent.
Puella Magi Yuuko Magica: Madoka is stated to be this by Kyuubey and Mami. Her appearant power tops all of the Puella Magi in the universe individually. Plus, she's got a mental link with Madokami. Of course, being who she is, she begins to assert A God I Am Not by a certain chapter.
RainbowDoubleDash's Lunaverse: Princess Luna falls squarely into this trope, as does Corona, The Tyrant Sun. Cadance falls right at the very bottom of this trope: While an order of magnitude more powerful than a mortal pony, she's still far weaker than her mother. It's implied that she'll eventually grow into this trope, however.
Shinji's Nightmare: Arguably Shinji once he truly becomes an Alicorn. He's capable of surviving in the vacuum of space, withstand atmospheric reentry with ease, and tests his telekinesis by creating a sphere over a kilometer in diameter of molten metal, concrete powder, and crushed glass, and throwing it into orbit thereby creating a second moon.
Sonic X: Dark Chaos: Maledict is an interesting Deconstruction. He's actually a Humanoid Abomination that was forced to take physical form in order to survive his injuries after his epic battle against Allysion that created the entire universe. And he's trying to keep his physical form at all costs, as dying will unleash his power and cause the end of the universe.
Thousand Shinji: Due to the events of the fic, Shinji, Asuka, Rei and Misato became the New Chaos Gods. They have a myriad of shapes, but usually wear their old human forms — or humanoid shapes — when they interact with mortals (their "public relations" bodies to put it another way). Their powers include immortality, psychic powers, and limited reality warping. Each one of them is attuned to a concept and has powers associated with it: Shinji, God of Trickery, has limited omniscience, the greatest psychic powers and shoots lightning bolts; Asuka, Goddess of War is super strong, super fast, nearly invulnerable and master of combat — armed or otherwise — and so on...
Transcendence: As far as most of Azeroth is concerned, Ichigo counts as one. Even bound to a vessel that severely limits his Shinigami powers, he regularly pulls off stunts that most humans couldn't hope to accomplish, and his latent spiritual power is compared to minor deities such as the Ancient Guardians and the Loa. One character even refers to him as "the young god". Ichigo doesn't seem to put much stock into this himself though.
In With Strings Attached, George meets and talks to Ardav, one of the Dalns gods. What this gender-less god's powers are is unknown, except that it can bring people to its home dimension, and that anyone who speaks to it cannot remember what it looks like.
At one point, thanks to the amazing mundanity surrounding the Dalns gods—their “worshippers” are more like employees and, in fact, don't even know what “worship” means—George speculates that they're actually phonies who set themselves up as gods. The various reveals about them during the book (e.g., they had a court fight over who was to control C'hou) leave the matter ambiguous, but they are definitely Jerkass Gods.
Given how powerful the four become, the trope could possibly apply to them.
Well before they get any power, John sardonically refers to the four as the gods of rock 'n' roll.
Wizards and witches are seen as this. This is true. But only when the Sword of Gryffindor (which acts Mjolnir in pretty much all but name, amplifying magic on an incredible scale) is involved.
Merlin may be one. He's a bona fide world jumper and time-traveller, as well as being one of the most powerful wizards in history, as well as possibly being The Ageless.
In Yognapped, the sibling gods Notch, Herobrine, and Rana are these to Minecraftia. They are, however, far from impervious to physical damage. Which is why Notch can stab the others In the Back and permanently kill them.
: Harry Potter is far more than just a powerful wizard; he's the "Master of Death and all that entails." Not only is he unkillable (or rather, he'll simply get better), Harry is also responsible for the deaths of all things. An example is when he stopped the Hogwarts Express from being scrapped. His intervention, preventing the "death" of the last steam engine on Earth, caused a massive resurgence in interest in steam power across the galaxy, such as the Asari creating a steam powered spaceship. Liara T'soni describes him as "the next best thing to omnipotent while being as far from omniscient as everyone else."Harry Potter: Death comes for everything. People die, yes, but ideas also die. Cells die, sanity dies, seconds die and in the end all answer to me. An accident preventing one such death resonated across billions of cubic light-years.