AKIRA is famous for this, thanks to the infamous giant fetus... thingy. It includes a final villain ultima-monster transformation, using it to introduce some fairly complex questions about humanity and monstrosity.
Attack on Titan has villainous and heroic examples, with the various Titan Shifters. Their transformations signal a major battle, often with plenty of carnage and destruction left in their wake. When Eren battles any of the enemy Shifters, the only thing his human allies can do is get out of the way. This is especially true when their Secret Identities are revealed, leaving them with no choice but to transform and fight.
Done interestingly in Bakugan. Season 4 Big Bad Mag Mel and his partner Razenoid turn out to be the One-Winged Angel incarnations of the previous seasons Big Bad Emperor Barodius and his partner Dharak after being exposed to the power of the Bakugan god Code Eve.
Berserk's Apostles typically have two forms. The first is their regular human form, often with some monstrous feature that serves as their "tell." The other is their full demonic form, which they typically go into when they want to devour a victim alive or when their regular form is not enough. Zodd has the form of a winged humanoid monster with a horned tiger's head and hooved feet, and later on in the manga loses one of his horns to Griffith and becomes his dragon. Grunbeld has the form of a powerful crystalline dragon. And Rosine has a "fairy" form in addition to her true demonic form.
The initial 'human' looking form is a mid stage, acting as a more inconspicuous but weaker version of their demonic forms, as their true forms are only revealed when they die when the power of the Behelit leaves them and they turn into the desperate (and usually dying human) that made a pact with the God Hand
When Sebastian of Black Butler reveals his true form, we don't get to see it, but it apparently includes black feathers and stripper boots, and is so horrible that Ciel is not allowed to watch. Ciel's seen some pretty messed up things.
The Arrancar transform (or revert back) into massive hulking demons when they release their zanpakutou. One of them even utters one of the page quotes above just before doing this.
Chad, a protagonist, had a similar line, "This is my right arm's true form," when he used his new ultimate technique, "Right Arm of the Giant", against the Arrancar Gantenbainne Mosqueda.
During Ishida's climactic personal fight against Mayuri—in which he gained a momentous amount of power temporarily at a permanent cost—he took on a literal manifestation of the trope, complete with a spirit-particle-absorbing wing.
Ichigo's bankai would also count as a heroic example of this along with the final getsuga tenshou that he used to defeat Aizen.
His hollow transformation is this mixed with an extreme case of Came Back Wrong and is one of the more terrifying hollow forms seen to date
Ulquiorra Cifer actually grows gigantic wings during his two releases. In fact, his final fight with Ichigo even ends with one of his wings missing, although he's really more of a devil than an angel.
Yammy Llargo, who grows gigantic, and reveals that his number is not 10, but 0.
Kaname Tousen, who becomes a huge bug creature, giving him sight(never had sight), then gets owned then appears to die in the span of 5 chapters.
"You never would have let me get an opening like that, when you were blind."
The Big Bad has spent 20 chapters or so gaining new "evolved" forms.
More recently, the Vandenreich have shown themselves able to use a more advanced form of Ishida's One-Winged Angel Form, with two wings and without the drawbacks.
All of the Chevaliers in Blood+, but especially James...
Spoofed on Bobobo-bo Bo-bobo. The villain Over has six lights on his chest that light up when he gets mad. When all six are lit up, he transforms into his true self... Torpedo Girl. Yes, it's exactly what it sounds like.
An enemy's true form being "Sambaman", an enemy whose method of attacking is... dancing the Samba. No, really.
Claymores can turn into one if they are willing to put greater reliance on the youma side of their souls. In this state, they become known as Awakened Beings, and each Claymore has a unique form, which can vary in appearance, which some possessing demonic or even animal features.
The Abyssal Ones (Or any other Awakened Beings that we see more than once) tend to run around in their human forms until they get into a serious battle.
In D.Gray-Man we get a good example of this when Tyki Mikk loses control of his Noah. He turns into an armored fiend with a good dozen tentacles coming from his back and a taste for blood.
Akuma could qualify as well, when they reveal their true form by shedding off the dead body of the one who tried to bring them back to life.
Recently, the Earl has transformed into an even more monstrous version of his usual appearance.
In Chapter 219, we see the Earl's true face; he's actually hot. And in Chapter 221, when we finally get to see the Earl's Noah power.
Digimon Frontier has a Big Bad named Lucemon who starts in the form of a child-like angel with wings and blonde hair and shiny light powers. He then turns out to be a fascist dictator and gets steadily deeper into One-Winged Angel territory over three new evolutions.
Between the various forms of the villains in other series and the increasingly (sometimes ludicrously) powerful Digivolutions on the heroic side in all series, Digimon loves this trope. The next best example is Myotismon becoming VenomMyotismon, a humongous and less intelligent form of Myotismon. In Season 2 he returns as an even stronger and more sadistic MaloMyotismon before he is finally destroyed for real.
Even a human has gotten in on it. Kurata, the Big Bad of Digimon Savers ultimately fuses with the Demon Lord Digimon Belphemon, taking direct control of it, his face appearing on its chest. Belphemon itself also counts, as this triggers its mode change from its cute Sleep Mode to its Kaiju-like Rage Mode.
And then there's Dragon Ball, though it typically happened on less grand a scale — the villain announces that he's changing to his "true form", then becomes larger and more muscular. (Some do this more than once!) The Saiyans have their Super-Saiyan forms.
In Dragon Ball Z, Frieza's initial form is small and rather weedy looking, but has proved to be extremely powerful in previous confrontations. He transforms into a much taller version of himself, then an even larger, monstrous beast with an elongated head and spikes on its back. However his much-hyped final form turns out to be just as small as his original, but more sleek and aerodynamic, effectively crossing the Bishonen Line. At first he is mocked for this, but soon proves that the extra speed and strength far outweighs what he lacks in height. And then these are followed by a more muscular form of the same, and after losing much of his body after his defeat on Namek and coming to Earth for revenge, a cyborg form.
His older brother Cooler, the villain of the movie Dragon Ball Z: Cooler's Revenge, starts the battle in the equivalent of Frieza's final form, but eventually, to Goku's shock, reveals that he discovered a fifth form beyond it, which he transforms into, becoming larger, stronger, and far more horrific.
Likewise, as Cell steps closer to his 'Perfect' form, he becomes steadily more humanoid.
Zarbon's case is an interesting one - in his natural form he is a large, ugly, and powerful hulking monster, but being obsessed with his own beauty, he most often uses a much weaker Bishōnen form. He is also incredibly reluctant to transform even temporarily into his ugly-but-powerful true form, and consequently determined to beat the shit out of the protagonist whose power forces him to do so or lose.
Majin Buu has the most transformations of any character in the entirety of Dragon Ball, as he assumes a new form and undergoes some personality changes every time he absorbs a person. He was created as a shrimpy little guy who has no vocabulary whatsoever and blows up planets for giggles; becomes very buff after absorbing the Southern Supreme Kai; turns fat and goofy after absorbing the Grand Supreme Kai (the form the heroes first encounter him in); expels the embodiment of its evil side as a pale, wiry thing; becomes muscular and savage when the evil side reabsorbs the good side; absorbs Piccolo and Gotenks to become smarter and more powerful with a more human face and longer antennae; reverts to a Piccolo-based form when Gotenks' fusion runs out; absorbs Gohan to take on his most human form yet; and then when Goku and Vegeta free all the fighters he absorbed he finally reverts back into his original form before all the transformations began. Counting Majuub from the anime-only Dragon Ball GT, that's 9 in total.
Buu crosses over into Power Limiter territory as The Grande Supreme Kai kept him from using all his power while also making him much more sane
Then there's the whole Oozaru thing. In an episode of the Saiyan saga Vegeta has a move that allows him to go Oozaru by creating a ball of energy that looks like the full moon — he uses this move and turns Oozaru. Amazingly he's still able to speak while being in this form, which was explained as him being trained to have some control over the form (as opposed to the only other Oozaru appearing being entirely untrained kids - Goku and Gohan).
And pre-redemption Piccolo grew building-sized at one point; same for Lord Slug.
Garlic Jr goes from looking like a paler midget version of Piccolo without the antennae (or like Emperor Pilaf) to looking like a bulkier, more adult-height version of the same.
Fairy Tail: The whole point of "Take Over" magic performed on oneself. Erza's Purgatory Armor is implied to turn the user into a demon somewhat; but we never get to see what it truly does despite her doing the usual "None have lived" boast that comes with a One-Winged Angel.
Envy's true form is... well, you'd hate to meet it in a dark alley. Or a light alley for that matter. It's a octopedal black-haired green thing, gigantic in size, with faces of the souls of its Philosopher's Stone squirming and screaming all over where its skin should be. However, this is also subverted. Envy's true true form, devoid of all the souls that compose it body, is that of a physically harmless embryo-like lump of flesh. It can still talk, and it convinces May Chang to return to Central where it can get "healed" (returned to its Eldritch Abomination form).
Downranked into a Clipped Wing Angel later when Mustang points out that the huge size makes it that much easier to aim at him. For that matter, the only other time he uses it in combat, against Marcoh, he is defeated with an attack which entirely ignores his physical might. He has much better luck playing the Shapeshifter Guilt Trip game.
Gluttony can open up his torso to reveal a failed attempt to recreate the Gate of Truth. Unusually he really is more dangerous in this form and his actual death in the manga and the Brotherhood series comes at a time when he is not using it.
Greed grows a black diamond skin over his body, which also sets off his sharp teeth to fangy advantage; he avoids using this form as much as possible, thinking it makes him look uncool.
Pride becomes a replica of the shadows behind the gate, a swirling mass of darkness, eyes and hungry mouths.
In the new Brotherhood anime (but not in the first anime nor in the source manga), Father Cornello transformed as well; he uses his Philosopher's Stone to turn into a gigantic version of himself, with an extra-monstrous arm where his alchemy had rebounded previously.
A subversion takes place in the final episodes of the first anime. In the middle of his battle with Edward, Envy finally reveals his true form. He actually looks a great deal like Alphonse... his younger brother... and uses the shock to kill Edward. A few minutes later, he plays the trope straight and turns into a giant snake (well, a serpentine dragon-thing at least) as he crosses the gate to get at Hohenheim. He gets stuck in this form when he reaches our world, where alchemy doesn't work.
In the manga version of Gantz, a couple aliens have this, but the most extreme example is the Nurarihyoon alien, who goes through quite a large number of different forms, each appearing after the previous form is seemingly killed. The forms vary wildly, from an old man, to a hulking horned beast, a demon-like creature, a floating ball, a giant naked woman made out of other naked women, and at least one more demonic form after that.
Stinger and Cohen from Getter Robo: Armageddon pull this at the end, fusing together and becoming some kind of planet sized Living Ship that can spew waves of Invaders.
Alucard from Hellsing uses this frequently in the form of removing his Power Limiters, to the point of not having much of a 'true' form. Paladin Anderson uses a nail from the Cross to become a thorn-monster. Also, Seras manages to pull off the One Wing (in place of an arm) look later in the series when Pip is killed by Zorin Blitz and she uses the blood he offers her to awaken her true vampiric abilities.
A heroic example can be found in the sixth light novel of High School DxD, where Issei goes utterly -berserk- when he is told Asia was killed, sprouting wings and entering Juggernaut Drive and quite literally -biting off the villain's arm- while growing swords and dragon arms from all of the jewels in his dragon armor.
The entire Living ShipGrey Geshpenst from Infinite Ryvius undergoes this process during the final battle, absorbing a bunch of Space Whales into itself and transforming from a normal-looking spaceship to a massive organic... thing.
Naraku is a walking process of One-Winged Angel; a shapeshifting conglomeration of demons, he's constantly rearranging himself and gaining more power, so that his current body is always a work in progress, and his humanoid guises (even the ones that are Actually a Doombot) are prone to bursting into a mass of poisonous vapours or tentacles. In the final battle, when he's close to reaching ultimate power, his body is that of an enormous floating spherical spider that may be even Bigger on the Inside and that the heroes enter, and after that his central humanoid avatar inside still goes through some more changes.
The mikura of Karas have this, transforming into mechanical monsters for combat.
Katekyo Hitman Reborn! has the Six Funeral Wreaths, a villain group who each have their box weapons embedded in their bodies. Their ultimate ability is to activate said weapons, which turns them into powerful half-animal beings.
And three of them end up getting tricked into activating their transformation just so their boss can absorb their power, in order to fuel HIS one-winged angel transformation.
In Magic Knight Rayearth, we have none other than Princess Emeraude herself. When Zagato dies at the hands of the Magic Knights, Emeraude loses it and decides to unleash her full power. This involves reverting to her actual adult age (her child-like appearance is a cover) and summoning a Masshin of her own - to fight the girls to the death.
Mahou Sensei Negima!. Subverted later on; after Negi single-handedly wipes out a gang of bounty hunters, the leader starts muttering about revealing his true form. Negi gives him a mean look, and he goes back to cowering on the ground.
This also happens to Negi when Kurt Godel revealed who was responsible for the attack on his village, and Negi's ensuing uncontrollable rage caused his Magia Erebea to run rampant and transform him into a monstrous black daemon whose only thought patterns are "KILL". He later has to go through Training from Hell so that he can actually control the power, rather than going into a blind rage. Its implied that "control" here means "it's turned on all the time" as a downside.
Naruto has this a fair bit. A couple of the purer "villain" forms of the transformation involved Gaara's grotesque mutation into his demonic Shukaku form, and Orochimaru's curse seal's second stage, which turns the bearer into a monstrous version of their former selves: various members of the Sound Five grow horns, spikes, deformed facial features, an extra eye, and a tail from using it(of course, some fans found Tayuya's 2nd form to be hot), and Face–Heel Turn Sasuke actually grows hand-like wings.
Orochimaru himself has a grotesque "true form" that he transforms into whenever he performs his body-switch technique. He takes the shape of a giant white snake made up of a multitude of smaller snakes, with a monstrous, dragon-like face and shaggy black hair. He also has a jutsu that allows him to transform into a giant "hydra", one of the mouths of which holds his normal body.
All the Akatsuki have a One-Winged Angel form in one way or another. Kakuzu's tentacle mass thing, Hidan's Grim Reaper form, Kisame's Samehada-Fusion form, Itachi and Sasuke's Susano'o, Madara's Intangibility form, Sasori's real body, Konan and her paper angel form... Pain and Deidara are the only who lack it.
And Pain already consists of six remotely controlled zombies; his final revealed form was a creepy wasted body impaled by many chakra antennae. Deidara did the thing mentioned in the trope description of becoming a living bomb.
All the Jinchuriki (except maybe Gaara) have this. They have their human forms, then the Version 1 (as Killer Bee called it) chakra shroud, which is still human, but has the chakra of his/her Tailed Beast creating a Battle Aura with the appearence of the beast. Then there is the Version 2, which makes the Beast's chakra burn their skin and making the tails solid, and has the risk of reducing the Jinchuriki lifespan if he doesn't have the beast under control. Then there is the change into the beast itself...
Spoof in Neko Majin Z, in which Neko Majin transforms in a way so subtle he is forced to point it out ("Look closer... I have double eyelids").
A few examples in One Piece. Virtually anyone with a Zoan fruit will have this to some degree, though only Rob Lucci and Kaku try fighting without their fruit powers. Most notable among these thus far is Tony Tony Chopper of the Straw Hats; whenever he transforms into his Monster Point form, it means trouble for whoever he's fighting. Especially now that, after the Time Skip, he can control its power.
Also, Eneru and Gecko Moria both go One-Winged Angel shortly before being defeated, with the former turning into a giant thunder god and the latter absorbing a thousand shadows to become a giant four-legged shadow demon...lizard...thing. Magellan when he uses Hell's Judgement to sit himself in a giant demonic skeleton of corruption that threatened to destroy the entire building he was in (this one was actually unbeatable, effectively being an Advancing Wall of Doom), and Sengoku the Buddha, who proves his moniker by becoming a giant golden Buddha statue with energy blasts from his palms.
Panty & Stocking with Garterbelt has Chuck and Fastener, who can turn themselves into a big hellhound or a dragon (respectively) by turning themselves inside out.
Pokémon may seem too casual an example to list here as Pokémon evolve all the time, but when an important character's Pokémon evolves to their final form right before (or even sometimes in the middle of) a huge battle in the anime, this Trope is definitely played straight.
Played even straight in Pokémon 4Ever where just right after Celebi is corrupted by the Iron-Masked Maurauder, it actually transforms into a giant monster made from twigs and leaves which for some reason resembled a Darkrai.
The final arc of the manga pitted the Nerima crew against a race of people who could turn into angel-like creatures (to be fair, they were genetic mutations from having drunk Jusenkyo water for generations.) But the Biggest Bad of them all, the one enemy that puts all of Ranma's prior foes to shame, started out as an obnoxious little kid who transformed into a living, breathing nuclear power plant with great golden wings and the regenerative powers of a Phoenix.
At least one fighting game used Pantyhose Taro's forms to its advantage by making him the final boss - Round One is against the human, and then he splashes himself with cold water before Round Two.
Hokuto does this near the end of the first season of Rosario + Vampire (manga version), after he tears off his holy lock that keeps him from losing his humanity.
Earlier in the series, Kuyo eventually shifts into what he considers to be his "ultimate battle form", which combines the strengths of both his "human" form and his monster form.
During the Land of the Snow Fairies arc of the second season, the group fights Kalua Shuzen. Berserker Tears dealt with everyone until Tsukune tore Moka's rosario and Inner Moka delivered a well-deserved kick to the jaw. Kalua's response is to remove one of her rosario earrings. Cue six or seven demonic wings sharp enough to cuts through Inner Moka's muscle, bone, and kimono and a full-power roundhouse kick not being enough to take her down. When Koko says "This is when she gets scary!", it's an understatement.
Happens in every Sailor Moon movie and the season finales.
Or at least the first and last season finale, in which Queen Beryl's dying body is possessed by Queen Metaria and becomes a... giant Queen Beryl, and Queen Nehelenia turns old and ugly (though this was a result of her leaving the mirror that kept her young, and this seems to weaken her, though she can still fight well). Though Germatoid should count, as he was the Daimon who was Possessing Doctor Tomoe, and is revealed to be a gigantic monster. Though not a season finale, Esmeraude is transformed into a dragon by Wiseman before Sailor Moon destroys her.
In Sailor Stars, Chaos first possessing Sailor Galaxia and then taking on his own form in the manga fits right in. As a less extreme version, the anime-version of Galaxia becoming very much like an undead beast midfight with Sailor Moon should also count.
Mazoku in general in Slayers all have this. All Mazoku can look human, the degree of which depends on how powerful they are. Low ranking Mazoku are easy to spot as they have monstrous attributes. Mid ranking Mazoku are a little harder, they look completely human, save for some traits that are off, such as a wrong skin color, but considering that there are talking animals in the series, it's not that big of a deal. And lastly, High ranking Mazoku look completely human. However, if they're pushed, they can transform into a "beast mode" which turns them into their real forms.
In the fourth-to-last episode of Sonic X's third season, Dark Oak, Black Narcissus, and Pale Bay Leaf use a Planet Egg and all seven Chaos Emeralds to merge together with an all-water planet with a tree on top of it to transform into a massive three-headed plant dragon resembling King Ghidorah from several Godzilla Toku films.
Also, the male Seedrians were shown to be capable of turning into giant Godzilla-like monsters years before five of them survived and became the five Metarex commanders.
An ongoing theme in Soul Eater, where there are living beings that can transform into weapons, retaining human form to interact with others and maneuver of their own will. They can also temporarily transform into an amplified weapon form by merging their souls with their Technician. Moreover, one of the major villains of the series (The Demon God himself) assumes a large, grotesque form during the last battle of the anime.
Practically a recurring joke with Arachne's ancient second-in-command, Mosquito. Every time the techs are about to beat him, he invariably reverts to stronger and stronger (younger) versions of himself, proclaiming each to be when he was at his "physical peak". (He pulls a Bishonen Line when he fights Kid. It's later subverted when he fights Noah. He goes into what he says is his most powerful form ever, and gets killed in about 3 seconds.)
The trope is so old and frequent, it has received numerous parodies for decades. Some time in the '90s, Soul Hunter even went ahead and lampshaded the common downside: "Villains who turn into a giant monsteralwaysdie."
Happens nearly every episode in Vampire Princess Miyu. The exception is the last episode of the TV series, where the final monster looks almost entirely human, making it somewhat less fine to kill her. The fact that the monster was Miyu's best friendChisato all along does not really help either.
Mazoku generals Drum and Guitar from Violinist of Hameln normally appear in relatively small and goofy-looking (although still extremely dangerous) forms, to conserve their finite amount of magical power/lifeforce. When pushed, they can transform into a city-sized, many-headed dragon and an horrific cerberus, respectively. Vocal, however hard this is to believe, after witnessing his Crazy Awesome acts of monstrosity is also sealed in a form that only utilizes 1/10th of his maximum power, however, in a subversion, his true form is a pretty boy version of him and exhausts most of his remaining magic in half a minute, causing Superpower Meltdown.
Xam'd: Lost Memories: A Xam'd is a person who has the ability to shapeshift into a humanoid creature with awesome powers such as Super Strength, Inhuman agility, and crazy bio-weapons (think blades and projectiles, not germs). This is more of a case of being Blessed with Suck, however, as these powers can also override a person's sense of self, resulting in them going Ax-Crazy, losing their memory, being turned into stone, or all three in no particular order. It's a constant danger for them, so it's rare to see a Xam'd make a full transformation; usually they'll opt for a Partial Transformation (Often just their arms).
In Yaiba, Kaguya transforms back to her true, gigantic form after she drains the essence of youth out of Sayaka.
Sometimes happens to individual Duel Monsters in Yu-Gi-Oh!, particularly the Winged Dragon of Ra.
Although in one episode Kaiba actually transformed into a Blue Eyes White Dragon.
In the manga (and Season 0 of the anime), near the end of the tabletop RPG against Yami Bakura, Zorc transforms into a super-form after his regular form is defeated. Yami Yugi even lampshades this by stating that, while horrifying, this is probably Zorc's last form.
In the anime, there is an arc where the main characters are trapped in a virtual world and fight the evil Noah, whose father is Gozaburo, Kaiba's evil stepfather whom he battles in the end. After Kaiba wins, Gozaburo transforms into a beast of fire, but Noah holds him back and both remain as the virtual world is destroyed. Somehow, Gozaburo survives just long enough to appear for a few moments in the real world as a beast of fire and part of the explosion, but they escape him before he can eat them.
Considering that the real-world island is exploding as Gozaburo activated it's self-destruct as a last-ditch effort to kill the heroes, and that Gozaburo became a beast of fire in the virtual world, the explosion taking on his beastly characteristics was likely meant symbolically than Gozaburo manifesting in the real world.
In YuYu Hakusho, Yusuke fights numerous demons, many of them start out fighting in human form, and then when they are losing they shift to demon form in order to increase their fighting power. Oddly enough, considering how violent demons are, many demons seem to prefer wandering around in human form even when there's no need to hide what they are (Hiei is a good example of this, since even when fighting the Saint Beasts in an all-demon town he says in his mostly-human form).
That is his true form. That's his body, it's what he looks like. He added the third eye through surgery. Since his behavior during his introduction was so out of line with the rest of his characterization, people have mostly concluded that stupid zombie-making sword was messing with his head, and that he normally knows better than to use the Jagan to cover himself with eyeballs, which may come with a power boost but means having weak spots absolutely everywhere. He's primarily a swordsman, after all.
In an amusing and well-deserved subversion/Clipped Wing Angel, Dr. Ichigaki gives himself an injection, transforming into a gigantic monster with extendy-claws. A pissed-off Yusuke annihilates Ichigaki in no time flat.
Younger Toguro still looks outwardly human most of the time despite being turned into a demon. He looks more like the demon he truly is when unleashing 100% of his full power. In the English dub, Hiei comments that he can't believe Toguro's body used to be human after seeing his transformation. Coincidentally or not, his demon form has a strong resemblance to Kairen the demon who slaughtered his students in the past (which became his Start of Darkness).