The Mega level also count as this, Devimon and the Ultimate forms of Etemon and Myotismon took forever to defeat, all 7 Mega-Level forms faced all got curb-stomped.
Slightly justified in that the kids were much stronger at the end of the series, (most of the time, anyway) and the stronger Digimon came right out to fight instead of sending in their minions, and as a result were killed much quicker.
In One Piece, two of the three notable villains to go One-Winged Angel were dispatched rather quickly thereafter. Eneru because he was too late and Luffy had already launched his ultimate attack, and Gecko Moria because despite his insane strength and giant size, he had sacrificed speed against the remarkably agile and super strong Luffy (also, his Villainous Breakdown sure didn't help).
Zoro even states that Moria's Shadows Asgard form more of a threat to him than Luffy; Now it's a race against time until the morning sun rises. Moria's just trying to run out the clock with that desperate move. Will we be wiped out by the sun, or will Moria destroy himself first?!
Much later, Caesar Clown merges with his own gas Shinokuni to become much bigger, much stronger, and much deadlier. Too bad for him, it makes him a much bigger target for Luffy's attacks.
For those who haven't read/seen AKIRA: during the endgame, Tetsuo's powers become exceedingly unstable and his body mutates and expands. It attempts to crush everyone near it, but at that point Tetsuo doesn't really have any control over his massively-expanding Body Horror. The psychics then teleport main character Kaneda away from the mass of flesh and proceed to blow it up.
Toward the end of the Three-Tails arc, Nurari fuses with two other members of the Quirky Miniboss Squad — Kiho and Kigiri — to form a gigantic blob-like monster. While, on their own, they had defeated Sai, Kiba, Lee and Tenten, and given Shino, Yamato and Kakashi trouble, Yamato manages to immobilize the fusion, which is then killed almost instantly by the Three-tailed Beast.
In Bleach, after revealing he's been made into a Vizard, Tousen Kaname says that he has a resurrection to go along with it. He turns into an insectoid monster, which also has working eyes. As he's about to finish off Komamura, Hisagi sneaks up on him and stabs him through the head. Hisagi claims that if Tousen hadn't been distracted by his newfound sight, he would have easily sensed him and dodged it. Yes, a blind man gained sight, only to be defeated by an attack he would have seen coming otherwise.
Yammy, despite initially seeming to be a Crouching Moron, Hidden Badass with his Resurrection transforming him into the unhinted-at "Cero Espada", really ends up falling into this trope; databooks explain Yammy's only power is he gets bigger and increases his reiatsu as his rage builds; the first and second Espada are considerably more powerful than the average captain, but Yammy's special ability only makes him a gigantic target that Kenpachi and Byakuya easily defeat offscreen.
Good guy version on Dragon Ball Z. Future Trunks thought he had surpassed his father by going past Super Saiyan - until he tries to use it in a fight. Sure he's big and strong, but the bulky muscles make him significantly slower and he immediately loses. Vegeta had realized that and focused on improving speed, rather than breaking through to the next level.
Ironically, Cell later makes the exact same mistake against Gohan, out of rage at being completely overpowered.
Happens to Frieza as well. After Goku transforms into a Super Saiyan, Frieza can barely even hurt Goku with only 50% of his power, let alone kill him. Goku gives Frieza enough time to reach his full power, at which point he is Goku's equal for a short time (though Goku was holding back to test Frieza and avoid causing too much damage while others were still on the planet). However, staying in that form burns up his energy at an accelerated rate. Because Frieza's already burnt so much energy from the arc-long fighting (as well as losing emotional stability at that level of power), Goku's greater stamina wins out.
In Movie 12, Broly is turned into something akin to an Eldritch Abomination due to a culture fluid, and despite this, he remains as much of a killing machine as before. However, he melts in the culture fluid and it seems he's dead. That is, until Goten, Trunks, and Krillin watch in horror as he arises as a gargantuan monster larger than a mountain and looks as if he could destroy the world many times over by simply breathing. Instead of an epic clash, he gets wet and is killed by the water. The heroes have no problem taking him out from there.
In Fullmetal Alchemist, Envy's full transformation is like this against Roy Mustang. The (possible?) increase in brute strength was significantly offset by the fact that his opponent was now so large that Roy barely needed to aim.
In a Slayers OAV, Lina and Naga are up against a powerful vampire. Partway through the battle, the vampire reveals that he hasn't been using his true form, and promptly goes into an impressively large transformation sequence... before promptly shrinking down into the form of a small bat. Lina gets annoyed and smacks it with a slipper.
The first battle between InuYasha and his full yokai half-brother Sesshomaru when he transforms into his true form (a giant demonic dog). Rather than rely on his tact, sword fighting prowess, and Dissonant Serenity in human form, the transformed Sesshomaru is much more blunt; he growls, stomps and bites like a dumb beast, including leaping headfirst into InuYasha's transformed blade, which destroys his left arm. Sesshomaru learned his lesson not to go One-Winged Angel on his opponents unless absolutely necessary, as his true form is seldom seen after that.
The big bad guy of the S-Cry-Ed anime, Kyouji Mujo, manages to gain the powers of a very powerful Alter and nearly kills Kazuma with it, only for Kazuma to get another powerup and throw him into the Alter Dimension. He comes back even more powerful and monstrous, but his powers are utterly useless and his giant form is incapable of dodging Kazuma's final attack.
A rather humorous example of this happens in Panty & Stocking with Garterbelt: a small ghost Panty and Stocking had spent a long time trying to kill earlier is turned into a huge ghost by Scanty and Kneesock, but Panty and Stocking kill her seconds later.
In Yu-Gi-Oh!, Yami Marik, after kicking Yugi around for most of their duel, ends up as a disembodied eye after paying almost all of his life points to make his Winged Dragon of Ra have an insanely high attack, only to have it removed by a card Yugi played face-down. Once regular Marik is switched with him, leaving Yami Marik in the eyeball form, Marik surrenders to Yugi, causing Yami Marik to dissipate into the Shadow Realm.
During the Onslaught crisis, when Professor Xavier went insane, combined his own powers with those of Nate Gray and Franklin Richards, and nearly killed the heroes of the Marvel Universe, the monstrous Onslaught soon became its own entity and separated from Xavier. But after getting his armour cracked by the Hulk, his "ultimate" form is revealed to be a cloud of psychic energy. He is killed within the next three pages, though not without the sacrifice of many of Marvel's non-mutant heroes.
During the Hellboy story "Darkness Calls", Hellboy is locked in a running battle against Koscheij the Deathless, who is unable to beat him, but who obviously cannot die. The Baba Yaga places more and more of her power into Koscheij, causing him to grow increasingly monstrous, until she is finally spent, and sacrifices the tiny remaining shard of Rasputin's soul she keeps with her. Koscheij becomes huge and monstrous, but the power quickly gives out, leaving him weak and feeble once again.
The sad fate of Igor Bromhead in the same storyline may count as well, though he's not actually trying to fight Hellboy this time, but rather begging for a Mercy Kill having mutated into a hideous monster.
An early defeat of the Absorbing Man (a Thor baddie) happened this way. For several issues, he repeatedly fought Thor to a standstill because he could duplicate Thor's abilities just by touching him. But finally he got impatient with not being able to just Curb Stomp the guy, and overextended his powers trying to absorb the strengths of the entire planet at once. Cue explosion.
This is par for the course for the Absorbing Man; he can match almost anyone, power-wise (he's repeatedly fought the Hulk and proven a challenge), but due to impulsiveness, carelessness, surprise or just plain idiocy, has to absorb something that just won't help and gets Hoist by His Own Petard. For instance, fighting the Hulk at a construction site. The building collapses, and he reaches for some rubble so he can become as sturdy as steel or concrete... and grabs a glass shard. You can guess the rest.
And then there was the first time he became water, and went insane when he blended in with the ocean. He has since learned how to control himself in liquid form, however.
In Universe X, we learn that the Absorbing Man managed to massacre the Avengers by absorbing the intellect of the super-intelligent android Ultron. This made him able to remember any form he took and shift around at will. Too bad for the Avengers the Vision didn't think of infecting him with a computer virus sooner...
The Absorbing Man has continued his fine tradition of absorbing the wrong power in the cartoon series The Avengers: Earth's Mightiest Heroes. The first time he, after fighting the Hulk with limited success as steel, transforms into rock. The Hulk immediately smashes his arms, pointing out that he can smash rock. The Hulk even sarcastically refers to him as "Einstein" for that move. The next time he absorbs Mjolnir. Which, to be fair, seems like a good idea, but overlooks the fact that Thor can control Mjolnir. And now he's got all its properties.
In the Deadpool Merc with a Mouth series, Absorbing Man is encountered alongside other zombified villains and heroes in the Zombie Universe. He proves to be the toughest challenge faced, even managing to survive the collapse of a whole building. Deadpool defeated him by tricking him into transforming into toilet paper.
Essentially, the main distinction Absorbing Man has regarding this trope is that he uses a different Clipped-Wing Angel form each time.
Films — Animated
Atlantis The Lost Empire: The Big Bad gets stabbed by a shard of magic glass and turns into crystal. He then lunges at the hero in his new crystal monster form, but the hero dodges, and the villain gets caught in some rotors and explodes.
Averted in Aladdin: The Return of Jafar. After being freed from the lamp by Abis Mal, Jafar's Genie form is extremely dangerous. During the final fight he quickly knocks out Genie, shatters Carpet into a million pieces, and turns the palace grounds into a lava pit that the heroes are almost burned alive in. They win only because of Iago's timely intervention and exploiting Jafar's single Achilles' Heel, destroying his dark lamp.
In FernGully: The Last Rainforest, Hexxus unveiling his stronger form doesn't help him much. Before he can even unleash his destruction, Crysta and the other fairies infect him with plant growth and seal him in another magical tree.
At the climax of The Flight of Dragons, Big BadOmmadon turns himself into a virtually omnipotent, grotesque hydra-like creature. Unfortunately for him, The Hero has just figured out how to use the rules of science and logic to nullify magic and, ultimately, destroy Ommadon himself. Turns out being the world's most powerful wizard doesn't help much when your enemy has just weaponized Doing in the Wizard .
Films — Live-Action
Calypso's transformation in Pirates of the Caribbean: At World's End, to an extent. She's far from powerless, summoning a whirlpool on command, but she has no physical body anymore because it turned into a mass of crabs, which promptly fell into the ocean.
In Wes Craven's New Nightmare when the archetype behind Freddy is defeated—in the humiliating way it had already been once before as the witch in the story of Hansel and Gretel—as it burns away it briefly turns into its demonic-looking true form, and a fat load of good that does it.
The Super Mario Bros. movie. After the titular heroes hit Koopa with a de-evolution ray, he transforms into a Tyrannosaurus. They then shoot him again, turning him into primordial ooze.
In the Sci-Fi movie The Hive, the titular army ants are able to form into all kinds of bizarre formations, such as mile-high tentacles. When denied humanity's technology (and one of the exterminators tries to frag the hive), they flip out and form into...a giant ant. All it does is badly injure the guy who tried to kill them, who proceeds to blow them up.
The Shredder in the second Teenage Mutant Ninja Turtles movie drinks the mutagen and grows into a gigantic mutant form...only to just as quickly bring down the dock above them. The Turtles emerge from the wreckage dusty but unharmed, and see Shredder's twitching hand rise from the rubble. Raph exclaims "No One Could Survive That!" and Shredder promptly dies.
When the One Ring is destroyed in The Lord of the Rings, Sauron briefly rises as a gigantic terrifying cloudy figure visible for hundreds of kilometers... and is promptly blown away and dispersed by a wind out of the West. Saruman did the same thing when he died, except the shade was man-sized - part of the repeating motif of Saruman as a far lesser version of Sauron.
"And as the Captains gazed south to the Land of Mordor, it seemed to them that, black against the pall of cloud, there rose a huge shape of shadow, impenetrable, lightning-crowned, filling all the sky. Enormous it reared above the world, and stretched out towards them a vast threatening hand, terrible but impotent: for even as it leaned over them, a great wind took it, and it was all blown away, and passed; and then a hush fell."
The wind is part of Manwë's domain so his power as the mightiest of the Valar might have something to do with it.
And both of them are lesser versions of Morgoth, whose shade still exists beyond the door of night and will come back some day to be Killed Off for Real.
Something very similar happens with the collective ghostly intelligence (assuming it is real) of the Overlook Hotel in The Shining. When the building explodes, a huge, black shape made of a myriad of tiny black motes, "like an obscene manta," seems to pour itself out of the window of the presidential suite and get ripped apart by the winds. Hallorann, the only witness to this event, is reminded of a time when he as a child blew up a wasp's nest with a firecracker and watched as the wasps rose from it in a collapsing, dwindling cloud, the single collective group intelligence of the wasps seeming to wonder furiously as it died what had done this to its home. He might have had exactly the right idea, considering the importance of the image of wasps to Jack Torrance. "This is what it's like to put your whole hand inside the nest."
Inherent in the The Mayor's plan in season three of Buffy the Vampire Slayer. He gets to be a completely invincible though average human for 100 days, before transforming into a giant snake demon which, though much more powerful, is destructible. Admittedly had he not enacted this plan he would presumably have remained a destructible human, so it's still an improvement. The downside is that the form needs a massive number of humans to maintain. To this end, he specifically tells his army of vampires that they have to keep the class near him so he can have a snack within reach.
Also occurs in episode "Fear, Itself" - The main characters are all trapped inside a fraternity house on Halloween where a demon named Gachnar makes them all experience their fears so it can feed on them and manifest itself. At the end of the episode the demon does appear with much shaking and spooky light...only to turn out to be smaller than your hand. Buffy defeats it by stepping on it.
The early Kamen Rider shows loved playing this trope with the Great Leader, the recurring Big Bad of the show.
At the end of the original series, Rider 1 encounters the Great Leader and rips his hood off, revealing a bunch of tentacles. Not pretty, but neither a real threat to The Hero. Rider 1 rips these off too, only to reveal a pale head with no features except for a large eyeball. And then? The Great Leader gives a final villain speech before he simply dies and disintegrates, leaving only his robes and eyeball behind, for no apparent reason. And then his base self-destructs. So technically, Great Leader undergoes not one but TWO Clipped Wing Angel forms without actually fighting the hero at all!
In the beginning of the next series, Kamen Rider V3, it is revealed that the Great Leader had faked his own death in the previous series. However, this series ends like the first, with V3 encountering the Great Leader in his lair - or at least, he thought so. What he finds there is only a skeleton with a still beating heart, completely immobile and not even quite alive either. The "final battle" consist of nothing more than V3 smashing it to bits within seconds.
The Government of Darkness in Kamen Rider X was led by King Dark, a huge metallic demon. In the finale, it turned out that King Dark was actually a Humongous Mecha, piloted by a rather puny Mad Scientist who was not even close to a match for X.
The final form of the Naughty Sorceress in Kingdom of Loathing, a sausage, can be this if you have the right item. If you don't, she's still stupid-looking, but can kill all but an insanely overleveled character (at least 5 times what is necessary to clear the game) in one shot.
And now no amount of leveling will help you, making it a Puzzle Boss as intended.
After you beat Crocomire in Super Metroid it falls into some acid and all the flesh melts off its body. Then, after an ominous pause, its skeleton crashes through the wall on the opposite side and the boss music starts up again... before the skeleton just collapses.
The SA-X's second form in Metroid Fusion is most definitely this. After defeating it, it transforms into a huge, scary-looking monster... that dies in three charged shots and has only one easily avoidable attack. The Core X it turns into after that is actually harder to kill.
This happens a lot in Resident Evil. G-Type, Nemesis, Marcus, Morpheus, Saddler... inevitably, the main villain's Lightning Bruiser humanoid form is much more dangerous than the slow, giant blob they inevitably transform into for the final battle.
Zig-Zagged in Resident Evil: Code: Veronica Alexia's first form is an agile human who can create fire, then her second form is a giant pulsating mass that is relatively easy to destroy, but when you do her top half breaks off and she becomes a smaller, fast, and agile dragonfly-like boss, which dies to a single shot from a linear rifle, but her final form is still more One-Winged Angel than other final bosses in Resident Evil.
It's arguable in certain cases; oftentimes the final boss cannot be beaten without some type of ungodly powerful weapon (for instance, Nemesis's final form requires a conveniently-placed railgun the size of a car to defeat).
The Golden Diva in Wario Land 4 doesn't look so tranquil once she's down to two hit points. And when she's down to one hit point, she's simply becomes... pathetic. She just becomes a pair of lips that doesn't deal any damage.
The finale of the final boss battle of Rayman 3: Hoodlum Havoc is André the hoodlum: a tiny black fly with hands. He flees from you. To defeat him, all you need to do is make a funny face at him.
Dhaos does this in reverse in the later versions of Tales of Phantasia, his second form being monstrous and his third being angelic, the result of him praying to his god for more power.
This trope is still played straight though in the fight against Dhaos. His monstrous form is difficult to hit and quite strong. The angelic form can be pinned down in a corner and incapable of fighting back.
The final form of Mithos Yggdrassil in Tales of Symphonia is the encapsulation of his broken body inside the physical manifestations of his own sins, weaknesses and fears — a form that is far weaker than his second, 'normal' appearance. Although it's still stronger than his first form as leader of Cruxis, thanks to its arsenal of attacks— some of which can hurt— he's a large target and doesn't get overlimits so he can easily be pinned down and combo'd to death. His low defense doesn't help either. This isn't really that odd, once you start thinking about it.
Additionally, he loses his 100% resistance to light magic, finally allowing Raine and Colette to do some serious damage (especially if you use Stardust Rain with Genis).
Devil May Cry has the demon emperor Mundus as a final boss. In the opening portion of the boss battle, he flies into space and Dante pursues him, afterwards, he knocks Dante down into a lava-filled arena. Then, after being beaten, he seemingly kicks the bucket; however, as Dante attempts to escape the crumbling castle, Mundus rises again; the statuesque facade he had used to fight you earlier is crumbling, revealing a grotesque blob of flesh and eyeballs. It's actually a lot easier to beat this form than when he was standing waist deep in lava. Additionally, in the first two battles, Dante stood a chance only because the Sparda sword's full power was finally unlocked; it was the only sword you could use against Mundus. In the last battle, Dante's able to hold his own with his weaker melee weapons — in fact, Alastor's Vortex can rip him apart with the greatest of ease.
After beating Sanctus Diabolica, the final boss of Devil May Cry 4, he merges with the Savior. Dante's fight with the Savior was epic, and Nero's fight with Sanctus Diabolica was as well, but the merged form goes down with three properly-timed Devil Bringer snatches.
Same thing happens in Devil May Cry 2 with Possessed Arius. Before transformation, the boss hits strong, has a couple of attacks which can be troublesome, and can perform sudden bursts of speed. After the transformation, as Arius-Argosax, it is confined to a single space, only really moving vertically, with maybe one attack that may be a threat, and that one doesn't really hit that hard. So it then becomes a simple matter of dodging it's ocassional attack and throwing stuff at it until it dies.
But then its FINAL form, The Despair Embodied, will absolutely murder you if you take it lightly.
Played with in The Legend of Zelda: Twilight Princess: After defeating a friggin' huge armored spider in the Temple of Time, the eye that was its weak point mutates into a small spider that runs around the room trying to stay away from Link, and it's easily beaten with a few arrows, or one pound from an animated statue. The surprised expression on Link's face as he sees the eye animate after he does his post-asskicking Victory Pose is worth a laugh.
How about an unusual heroic version at the end of Twilight Princess? Midna finally uses the game's previous Plot Coupons to transform into some sort of giant Twilight spider creature to put an end to Ganon once and for all. Ganon is seen shortly afterward, crushing her Fused Shadow helmet in his hands. She gets better.
Similarly, after destroying Trinexx's fire and ice heads in A Link to the Past, it turns into a weaker snake-like form.
In Pikmin 2, the TitanDweevil initially has four weapons, each being one of the game's main hazards. Once you remove all of its weapons, it sheds its metal coating and has a more crab-like appearance. It can't do anything to kill your Pikmin, but getting to use all your Pikmin on it at once on top of the Crowning Music of Awesome makes it a glorious finish to the battle. Again, Tropes Are Not Bad!
There's another enemy named the Waterwraith, a strange humanoid creature that rolls around on stone wheels. It's an invincible monster until its weakness is exposed; purple Pikmin. It goes from it chasing you to you chasing it by the end of its fight.
The final final form of the final boss in Parasite Eve. After three forms of extremely creepy evolution to One-Winged Angel form, it turns into a giant goopy green thing. It can still attack, but is much weaker and will go down with a couple of shots from your special Chekhov's Gun. How does this happen? It evolved into a defense-focused form and you could not damage it at all until you got special gun clips with Aya's cells inside.
World of Warcraft has Kael'Thas's second encounter. While he definitely looks more intimidating due to the way a demon saved his life, he's a far shot from his former self, who had several servants, animated weapons and a very impressive event heralding the last stage of the fight. Instead, he only goes through the last two stages again, the second of which was weakened so much that any single class with self-healing capacities can finish him off. He also went from a 25-man raid down to five people, but even for that he's not particularly impressive compared to the rest of the dungeon he was in. People were more likely to have troubles with the last pack of regular enemies. The reason is because Kael'Thas hasn't gotten any stronger due to the demon's interference, it was just a matter of making out of his defeat alive. The crystal in his chest is preserving his life. You're fighting a guy on life support.
Also, while less dramatic, High Astromancer Solarian's fight. The first phase involves her casting deadly arcane spells and summoning adds galore. Upon hitting 20% health, she seems to go One-Winged Angel by transforming into an immense Void Walker demon... but the encounter actually turns into a Tank-And-Spank fight and can be won with merely a handful of raid members alive.
Played with in Shogo: Mobile Armor Division. After you blow up his mecha, the Big Bad's final form is simply himself on foot. While you're still in a 50-foot mecha. You can simply walk up and step on him.
Actually, you'll have to fight the Big Bad on his mecha and with him on foot in both endings, but in the other you'll have to fight him on foot yourself. While he is on his mecha. Even then, he is able to take so much more bullets than any other human opponent in the game that is looks like he's cyborgized beyond humanity - he doesn't bleed the way humans do. Even when you're on your mecha, you'll have to step on him several times to kill him for good.
Sephiroth in Final Fantasy VII had a full meal of a Sequential Boss battle. Appetizer: a creepy look that is a pain in the ass to battle. Main course: theOne-Winged Angel, Safer∙Sephiroth, with Crowning Music of Awesome by that name - which is still be a pain in the ass to battle. For dessert, give yourself one HP and initiate a one-on-one battle with a SOLDIER who has a full Limit Gauge and a BFS. The only thing that saves the final battle from being horribly anticlimactic: FMV graphics and Omnislash.
In Final Fantasy X, after fighting your way through the guts of Sin, Yu Yevon's giant monster body, and killing his physical incarnation (actually a transformed version of the hero's father), Yu Yevon himself turns out to be a floating spider symbol that can't even kill you, since your team has auto-revive on for the duration of the final battle.
Final Fantasy Tactics has a variant on this, where the Demonic, supposedly stronger forms of certain boss characters are actually much, much easier to deal with than the human forms. Elmdore and his Assassins: In human form, they're insanely fast, with hugely damaging skills and unblockable one-hit-kill attacks. In their demon forms, they're much slower, and go down easily.
Final Fantasy XIII 's final boss, Orphan, has two forms. The first requires a great deal of luck and strategy to defeat even with the right accessories on the party leader, especially when underleveled; the second can easily be defeated within 2 or 3 Paradigm Shifts.
In Grandia II the first fight with Pope Zera is a major contender for hardest boss fight in the game. However, when facing him again after the Boss Rush with the pieces of Valmar, he's a pushover with only 1 attack able to cause serious harm.
Justified by the fact that you've destroyed most of Valmar, leaving nothing but an insane human, who thinks he's much stronger than he actually is.
In Grandia I, Gaia Core is a tank, and will happily trade heavy blows with a well-leveled and equipped party; but get past him to the FINAL final boss, Evil Gaia, and all you've got to worry about are random minor status effects, like poison. Maybe if they came at you in the opposite order... but for all intents and purposes, Gaia Core is the final boss of Grandia 1.
At the end of Indiana Jones and the Fate of Atlantis, Indy convinces the evil Colonel Kerner to try the ascension machine in lieu of using him as a guinea pig. As it activates, he becomes taller and taller, his eyes glow, and he can feel the power of godhood surging through him when— he suddenly crumples into a misshapen little imp. Horrified by his appearance, he kills himself by jumping into the lava. Par for the course in an Indy climax.
A minute later, the evil scientist Dr. Ubermann undergoes the exact same fate when Indy convinces him to step into the ascension machine too. Ubermann does succeed in transforming into an energy being, but the raw power is too much for him and he quickly dissipates into nothingness, taking Atlantis with him.
Copy X from Mega Man Zero really went One-Winged Angel at the end of the first episode. In Zero 3 he tries to transform again, but Dr. Weil set him up to self-destruct when he tries.
Ys: In II Eternal, Darm regresses to a winged sphere form for the second half of the battle. In Dawn of Ys, Arem turns into a large immobile purple Blob Monster for his final form, which is a cinch compared to his previous Marathon Boss forms.
In The Legend of Dragoon, when you invade the lower floors of the evil empire's castle, you're spotted by a scientist, who says that he's worked on a new transformation spell that he'll use to kill you. The creepy pre-boss music starts up, and he transforms into a dog. Dog doesn't even try to fight you, it just barks. One of your party members- Shana- even comments on its cuteness.
Andross sort of suffers from this in Star Fox 64. To wit: this is a battle fought in All-Range Mode, and Andross's Brain has no ranged attacks. It's just a matter of shoot the weak spot, fire one shot at the main brain to make it teleport away before you crash into it, U-turn to face it again, repeat. Just so long as you don't mess up and get both wings blasted off by his Brain Tentacles, which will do their damndest to never let go. Messing up is not exactly unheard off, however, since Andross's Brain is fast, faster than your Arwing without boosting. Sometimes the battle comes down to who's the better one at maneuvering.
After defeating Belial in Gradius IV, its eyeball morphs into a replica of the Zelos Force from Salamander/Life Force, and fires laser beams everywhere, but then explodes.
In Tekken 3, True Ogre is usually regarded as one of if not the weakest character in the entire game. This is especially jarring considering the original form is very hard to beat.
In Sa Ga 2, abusing MAGI can turn you into a god, complete with a One-Winged Angel form, and the more MAGI you have, the more powerful your new form is. The game's second-to-last boss, Apollo, managed to get his hands on all but one of the MAGI, and ends up being a very difficult fight. However, because he's missing a MAGI, his new form is unstable. Even if your party isn't strong enough to kill him with damage, if you simply manage to survive enough rounds of combat, he'll eventually undergo a Superpower Meltdown and explode.
In Haunting Ground, your nemesis seems nigh-invincible, having infused himself with the rejuvenating immortality elixir known as "Azoth." He regenerates from a creepy wheelchair-bound man to a healthy young man capable of zapping you with magic, and throwing him into a pit of molten metal doesn't stop him. This is where he enters his "Clipped Wing Angel" mode, though; he's now ON FIRE and can kill you just by touching you. Since he's on fire, as long as you can (barely) manage to stay ahead of him, he will eventually burn to a crisp.
The Demon Beast from Chibi Knight. It has three stages. First, you need to destroy its shield orbs before you can even hurt it. Then it takes on a different pattern when it loses its shield. The third form is a giant eye that just sits there and does nothing.
Oogie Boogie in Kingdom Hearts, after you beat him the first time, absorbs his entire house and turns huge with the power of darkness. But he just sits there, barely even scratching you as you take out his power sources one by one. Even the random Heartless Mooks hanging around there do more damage!
Kingdom Hearts: Chain of Memories: You first fight Marluxia in a difficult standard Org. fight. He's a lot like Axel, with his fast, varied, hard to predict attacks, and the ability to easily punish you for any mistakes. Then he hops into some kind of flower mecha, loses all his good attacks, and just becomes a tedious, easy to handle boss who always gives you time to heal. Ansem in Riku's mode seems like this when you fight him in the middle, but in the GBA version when you get to the end you'll find he is a worthy final boss.... however the PS2 remake made it much easier to dodge and block his attacks.
The PS2 remake played with it a bit. Marluxia has a 3rd form, which just sits still and takes only a handful of Keyblade slashes to take down each health bar. The trick? He has several powerful gimmicks, such as making you drop all of your attacks, shooting you with a laser attack that will hit about a dozen times if it connects right away, or casting Doom on you. Also, nearly all of his attacks are Sleights, meaning if you don't have the right cards, you'll be left desperately trying to dodge them.
Kingdom Hearts Birth By Sleep: The first time you fight Xehanort he's slow, predictable, easy to dodge and goes down fast. Then you fight him again, he's fast, has loads of incredibly powerful attacks (a long, devastating combo, and METEOR SHOWER (not the Shotlock, but a variation of Meteor instead) which is an auto gameover if you don't have the right abilities, a ridiculous amount of health and the ability to easily kill you if you screw up. Then in the epilogue you fight that version again before he changes form gaining even more health!.... and trading Meteor Shower and a lot of his more annoying moves for a bunch of slow, easy to dodge attacks, and going from constantly pressuring you, to always giving you enough time to heal.
On the other hand, Xehanort gains some really nasty attacks, like the ability to hold you in place while he goes to town with a sword combo.
Most of the game Blood II the Chosen consists of chasing after a mage named Gideon. When you finally fight him it is a nightmare. He flies, teleports seemingly at random, casts spells and fires laser beams from his eyes. If you win you enter a spirit realm and meet him again when he transforms into a large spider. This is almost immobile and spits slow moving acid. A bit of bog standard FPS strafing and down it goes.
Ōkamiden's final boss has one of these as his third form, as he tries to possess Kurou. It turns out Kurou is a living doll made by Waka for the sole purpose of sealing away the Big Bad, and when Kurou is destroyed, so is he. It's still extremely difficult, though... for a different reason.
Baten Kaitos: Eternal Wings and the Lost Ocean has the Post Final Boss, Geldoblame, who is a massive earthen head sprouting from the ground. He has a tremendous amount of HP, but his attacks are laughably puny and a hit from a Spirit Attack is an Instant-Win Condition.
Fadroh could be seen as a subversion. After he transforms into a giant demon, he hits on par with the mooks in that area, but then he busts out the Orb of Magical Offense, which jacks his damage to quadruple digits and lets him move twice per turn, which turns him into a proper One-Winged Angel, as well as the game's biggest That One Boss.
In Shin Megami Tensei: Strange Journey, the Final Boss of the Neutral and Law endings subverts this. After defeating her first form, she is reduced to an embryo-like form, incapable of achieving her goal of transforming the Earth into a new world with the Schwartzwelt. However, she becomes a lot more powerful in combat and picks up a few new skills, including a 100% accurateOne-Hit Kill attack. Unless you're sufficiently leveled up and know what you're doing, you're going to die.
In the campaign modes of Dawn of War Dark Crusade and Soul Storm. After gaining all the wargear upgrades for your Chaos Lord, you have the option of gaining one last piece of wargear that turns him into Daemon Prince, the ambition of all chaos worshipers. It's not worth getting, while a Daemon Prince in an improvement over a Chaos Lord in a normal game, but by the end of the campaign the Chaos Lord in either campaign will have gain a massive increase to his damage per second, and will actually be higher than a what he'll have as Daemon Prince, and becoming a Daemon Prince causes him to lose any abilities his wargear gives him. The only thing gained is an HP boost, which is not worth it.
In the final Bowser minigame of Mario Party 5, Bowser consumes a potion that causes him to grow to Giga Bowser-proportions...only to crash through the floor and get stuck.
One of the most infamous in Sonic lore to date is the final boss in Sonic Chronicles: The Dark Brotherhood  where, despite the fact that the previous battles have you nearly drowning, incapable of using POW attacks, and even fighting with only one character, the final battle against Lord Ix can be done in twelve seconds if you can match every combo on the touch screen. What makes it even more ridiculous is that the touch screen commands are arguably easier to follow than most Mook characters' attacks.
This is subverted in Onimusha: Dawn of Dreams. The final boss starts off as a massive god you beat rather easily using Soki in his Black Onimusha form...but he's not done. The second form take the guise of the man in white who appeared so often in the game and you have to fight him with your allies. You'd expect him to be easier, except now he has a stupid amount of health, is hard to combo on and can't even be hit until you destroy enough rocks in the area while avoiding their annoying attacks. It's not so much hard as annoying and long.
Subverted in Mother 3. Porky goes through a One-Winged Angel phase first, appearing first as a normal chubby boy, and second as a feeble yet immortal old man inside a huge mechanical spider. But at some critical point during the final battle, Porky seals himself inside an "Absolutely Safe Capsule". While inside, he can't do any damage to the protagonists—or anyone for that matter. However, he's invincible in this form—though in a way he's "defeated" at that point because said capsule is inescapable, meaning he's stuck inside forever.
Loewenzahn in P.N.03, after its initial two forms are defeated the second time, transforms into a mecha-phoenix as a last ditch effort. Its attacks can easily be dodged, and it goes down quickly.
In Skies of Arcadia, after a normal battle, then a difficult and rather tedious airship battle against a giant silver...thing, Ramirez attacks you on the deck of your airship for one final battle, semi-transformed into a monster. However, it's easier than the previous two battles, and combined with the Crowning Music of Awesome, it makes a for a fun beatdown. In addition, Ramirez has a rather amusing attack, Silver Nightmare, that forces one of your characters to use a technique against your party. More fun than it sounds, as it usually doesn't hurt them that much.
A couple of units in Gundam Extreme Vs will change into a "heavily-damaged" extra form upon being destroyed. This form only has 100 health and generally very few methods of attack, but it allows the player to try for a last-ditch attempt at defeating their enemy.
This is a derivative of the Recover Awakening featured in Gundam Vs Zeta Gundam: if your Awakening meter is full when you or any of your allies take a hit that would be fatal, the subject is instantly restored to 25% health at the cost of one of its extremities and any weapons attached to the lost limb/head/binder. However, enemies never use the Awakening system so that's another trope.
In FTL: Faster Than Light, after losing its cloak and drone control unit, the Rebel Flagship redirects power to its shields, teleporter, and 'some kind of superweapon'. The shield turns out to be a super-heavy Zoltan Shield, the teleporter is a two-man unit that only sends humans, and the superweapon is a barrage of eight or nine heavy lasers. Without the Halberd Beam, the Boarding Drone, or the Drone Swarm, however, most players breeze right by it.
The final form of the final boss in Dynamite Dux is very tiny and can't attack - he just runs around real fast. Though he can take off a third of your health through Collision Damage, this is nothing compared to his previous forms.
In Kid Radd, Gnarl can transform into what would be a very impressive cyborg if it weren't for the total lack of legs. Later, the Seer merges with Crystal and several other powerful sprites, and as he's defeated mocks the heroes for thinking that beating him in a video game fight would defeat him. However, because the Seer forgot to fuse with an NPC, which would have given it invulnerability, it is able to be beaten. But because each sprite has a different idea of what subroutine should be activated when they're defeated, the Seer freezes, effectively being Killed Off for Real.
In The Adventures of Dr. McNinja Dr. Birding shares the ability his son has, to transform into a giant purple monster. However, Dr. Birding is paralyzed and remains so when he transforms, but no longer fits in his wheelchair. So he can no longer move even with artificial aid.
In an episode of The Powerpuff Girls, the girls are shrunk down to fight an army of nanobots too small to for a normal sized person to harm. When the girls start winning, all of the nanobots merge into one monobot that manages to completely overpower the girls, but is also now large enough for the normal-sized Professor watching the fight to destroy simply by stepping on it.
In an episode of The Thirteen Ghosts Of Scooby Doo, the villain gets frustrated as Scooby uses the McGuffin to counter all of his spells. Having enough of this, he makes himself really huge, where he inadvertently gives Scooby turns himself into a fly to evade him. Malidoor turns himself into a toad to catch Scooby, but in this form the tag along just walks up behind him and puts him back in the Demon Chest, the can that was sealing his evil.
In Ultimate Spider-Man, Spider-Man confronts Nightmare in the dream world, at first he see's him he's a muscular demon with flaming hair, but after Spidey gets the upper hand of Nightmare, he is reduced to a skinny, bald whelp.
In Getting Back on Your Hooves, after the villain has failed to demoralize the Mane Six inside the dreamscape, she tries to intimidate them by assuming the form of an alicorn. It doesn't work, because they fought and defeated Nightmare Moon, and recognize her for the fake fraud that she is. While her initial tactic of predating on their fears and insecurities could have worked, this move just gave them a big stupid target they could beat up without remorse.