Usually, Shapeshifting is done quickly and without undue damage to the shifter. For whatever reason, the body flows from one form to the other without much trouble. But that isn't always the case. Sometimes, those who would take on another form are going to suffer for it.
As the name implies, a Painful Transformation tends to be agonizing. While it may not leave permanent injuries, it's still not pretty.
There are generally two ways transforming can be painful:
Physical - The body is tortured during the transformation process. This is rather understandable, as one would imagine the bones and organs shifting around as having some sort of impact on the nerves.
Mental/Spiritual - The user's mind is overrun with horrid... whatever. We rarely get into a shapeshifter's head. Externally, it looks like they undergo a Freak Out every time they change shape. This may even be necessary to transform, in cases like that of the Incredible Hulk.
When the title character of Naruto releases his Demon Fox power at the four tails level, his skin peels off before burning into ash, and blood covers his entire body to form the Kyuubi's body. Also, he loses consciousness because of the injuries to his body, and the Demon Fox takes control of it. Changing back is also incredibly painful as he temporarily has no skin.
Even the lesser forms are painful to an extent. The chakra is poisonous to Naruto and constantly burns his skin, only the accelerated healing it grants preventing him from succumbing to the damage.
At least those work like they're supposed to. It gets worse when her best friend forces the transformation.
The Beast Spirit Evolutions in Digimon Frontier have a painful yell as the characters evolve. Ko(u)ji in particular will sometimes suffer pain and/or weakness after de-transforming, whether the transformation was painful or not, leading to Fanwank about what just what it is that makes it so hard on Koji alone.
Adding to this, Koji and Koichi most likely go through the most painful transformations of them all. This is because the beast spirits do bend their bones, flesh, and bodies to match their evolution. Everyone else is human shaped while they have to suffer a complete bone re-structure.
Although not quite as much, the Digivolution sequences in Tamers show the Digimon in slight pain as their skin is peeled off.
Hayate's similar transformation at the end of A's appears similarly painful, but as her body is at this point being controlled by an AI, it seems unlikely that she felt it.
Valgaav (Slayers TRY) is capable of a partial transformation into his dragon form. The transformation appears so painful to him that he never manages to transform fully.
In s-CRY-ed, Kazuma and eventually Ryuho, Martin Zigmarl and Straight Cougar damage their bodies when they go into their alter forms. Usually, the scars appear where the armor does. For example Kazuma gets scars on his arm, then on his face and even part of his hair starts to change. By the end of the series, he doesn't even open his right eye unless he's in his alter form (which he might possibly not even have outside of his alter form). They look pretty scary during the last fight.
Hiwatari's transformation into Krad in D.N.Angel is very painful, one of the factors being the fact that he usually fights it quite hard. Contrast with Daisuke's relatively easy transformation in to Dark, only experiencing pain for the first time and when he grows his own wings in the final episodes.
In the manga, Daisuke feels pain when transforming after Risa was kidnapped off the Farris Wheel because he transformed with anger, not love. This could also explain why transforming is so painful for Satoshi. The one time he did transform with little-to-no pain was after diving to save Risa when she fell off the tower, transforming out of "love" (according to some fans).
Tsubasa's first transformation into Figure17 seems to cause her pain for unknown reasons, although as she's presented floating in some kind of Cyber Space enviroment, it might be purely mental.
Mamoru Kusanagi from Blue Seed bleeds green blood when he brings out his arm blades.
Every time the titular character of Howl's Moving Castle transforms into and out of his bird form, the experience gets more painful and difficult.
While it is inconsistently portrayed (at least in the manga), the more extreme renditions of Chise's transformations into the Ultimate Weapon in Saikano are agonizingly painful for her.
The titular haibane of Haibane Renmei are born looking like normal humans, until their wings grow during their first night in the town. Having a pair of wings explode out from one's shoulder blades is about as painful as it sounds.
A lot of this in Arc The Lad, as for chimera transformations. A lot.
No transformation fits this trope better than Tetsuo's mutation in AKIRA which also may be one of the most over-the-top examples of Body Horror ever depicted.
In Blood+, the transition from human to chiropteran is not pleasant. For example, when Saya is forced to turn her little brother to save his life after her Psychopathic Manchild of a twin sister nearly kills him, Riku just convulses and screams his head off before blacking out.
In Dragon Ball Z, Frieza's transformations in particular tended to involve a lot of screaming and incredibly painful-looking contortions. Buu's final transformation consisted of nothing but standing around and screaming for a very long time, but that may have been less physical pain and more that he was devolving from a fairly intelligent Ax Crazy to a mindless Eldritch Abomination.
Ditto for Goku's first-time Super Saiyan 1 and 3 transformations.
Eureka'swings growing from her back was not a pleasant experience.
In Detective Conan, Shinichi's transformation to Conan is painful each time he goes through it. Understandable, as his body was literally undergoing apoptosis.
To give some idea, he constantly describes his de-aging as feeling like his bones are melting and begins to sweat profusely while clutching the left side of his chest, like he's having a heart attack. The first time he re-aged, he ended up bedridden and thought he was actually dying. Both types of transformation also cause him to burn up so much that his body is literally smoking as it happens. Poor guy.
Even though Ichika's later transformations in Uta Kata are perhaps not physically painful as such (although she tends to become nauseous), they are extremely unwanted and emotionally scarring.
Evangelion Unit 02's Beast Mode in Rebuild of Evangelion 2.0 requires of a painful realignment of the spine held in place by 10 pylons, all fed back to the pilot via Empathic Link. Mari was very visibly affected by this.
Transforming into a Hollow in Bleach seems to be an agonizing process, if the Pluses' reactions to it are to go by.
Not sure if it counts as a transformatoin, but in Hell Girl season 3, Yuzuki after being possessed by Aigoes through a sureal sequence where she convulses and screams as the egg-thing comes out of her back.
The replacement of lost limbs with automail is said to be incredibly painful, and the scant few flashback's to Ed's experience with the procedure show him crying and groaning in agony.
Late in InuYasha, the title character is forced to use a Jewel Shard on the Tetsusaiga to give him a power boost; however, the jewel becomes corrupted and forces him to transform into a fulldemon. Given how much he was screaming, it's safe to assume the forced transformation was pretty damn painful.
This has become a problem for Jaime Reyes the Blue Beetle.
The Incredible Hulk transforms extremely painfully in most instances, which is probably why Banner's attempts to keep control tend not to work once it's actually started. In his case, the pain is mental as well, as he can feel his human intellect degenerating.
The 1986 version of The Fly, after a slow, humiliating and painful metamorphosis from a healthy man into a sickly decaying half-insect wretch, Jeff Goldblum's gruesome and heartbreaking final transformation into "Brundlefly" has his skin peels off in chunks, joints crack audibly into reverse position, and his skull splits open to reveal its new insect shape.
In Disney's The Little Mermaid, Ariel's tail is literally torn in half as she is changed into a human. The facts that it occurs in silhouette and the two ragged halves become shapely legs almost instantly does little to ease the horror of the scene.
And of course, Disney being what it is this is actually toned down from the original fairy tale; not only was the transformation excruciating, but afterward she felt like she was walking on knives the entire time she was transformed.
Bavmorda's "You're all pigs!" spell in Willow cannot be described as pleasant.
The first transformation sequence in The Company of Wolves, wherein a werewolf, having disappeared for several years, flies into a rage over being forgotten by his lover. He begins to tear his own face off before his flesh splits open by itself, revealing the intricate details of the human anatomy for a few moments before the muscles and bones begin to twist into the shape of a wolf's, the visceral display traumatizing the woman's children all the while. Then his former lover's husband returns to the house and beheads him. His head goes flying into a vat of milk, then resurfaces as a human head, his blood staining the milk pink. Delicious!
In Dog Soldiers, the transformation into a werewolf is apparently very painful, as the unfortunate lycanthrope-to-come begins screaming and grunting as they stagger around the room, tripping over random objects, as fur begins to grow and they generally display more wolf-like characteristics as the change continues, growling instead of crying for example. This occurs is a surprisingly dramatic sequence towards the end of the film, where the infected character of Sergeant Wells is writhing around the kitchen as his accomplice Cooper makes his escape. Eventually, towards the end of his change, he attracts the attention of the remaining werewolves, looks at a picture of his wife, roars and blows the fuck out of everything in the house, including him, with the faulty gas cooker he was leaning against.
In Makodap's short film 11, the main character Peter Baxter attempts to flee from a luxury resort without paying his bill. He is tricked by the company and is painfully transformed into an attractive young woman. The painfulness of the transformation is intense with Peter screaming in agony, as bones break and reform. The company intends to get their money somehow, and have plans for Peter, or Nikki as he will be known as.
Johnny Blaze's first transformation into the Ghost Rider has his skin burning and melting off. He goes beyond the point of screaming in pain and winds up laughing maniacally before the process finishes. Subsequent transformation are instantaneous and seemingly painless—unless the Ghost Rider just doesn't acknowledge pain.
Sebastian becoming invisible in Hollow Man, as well as making the previous test subject visible again.
Ron Howard wanted something like this originally for the bathtub scene in Splash where Madison the mermaid turns into her mermaid form in the bath. But he feared that it would ruin the appeal of the character. But the part where her lower torso bubbles and turns scaly would probably count- seeing as the bath tub scene in general was intense.
The Mask. The first time Stanley puts on the mask. All the times it occurs later it's off-screen, for a good reason.
The animated series also had some of it, but mostly while he's removing the mask. Which is only sensible, since pulling the mask off basically requires him to tear off his face.
The Mask Pressbook has this to an extreme in their test images of Jim Carrey turning into the Mask. One of them looks like it was borrowed from The Howling or American Werewolf In London. There are pictures on that on Jim Carrey Online.
In Innerspace, Tuck uses a proceedure on Jack to reshape his facial features to disguise him. He warns him beforehand that it will hurt, and it certainly does. (And hurts even worse when it wears off and his face turns back to normal.)
The poor title character of the dark and edgy Kamen Riderdeconstruction film Shin Kamen Rider: Prologue suffers from this. Rather than simply having the 'armor' appear over his body, Shin's body actually changes, distorts and morphs into the Shin Kamen Rider. This is only done twice in the film, and is extremely painful for the guy (also leaving him naked for some reason); specific super-creepy examples include his forehead splitting open four ways at once, and his jaw splitting in half. They had to tone the costume down a bit for his appearance in Kamen Rider Decade, and even then he was pretty scary-looking.
In Troll, when Torok injects Peter Dickinson (Sonny Bono) with his ring to turn him into one of his minions, he turns bright green with slime oozing from cuts on his body while screaming in agony the whole time, morphing into a cocoon which cracks open. Out pops a little monster with Peter's facial features and spider legs.
Using the shape-shift drug polymorphine doesn't look like much fun if agent Lechias' face in Damnatus is anything to go by; not to mention that just to start the process you have to stab yourself in the stomach with a big friggin' needle.
In Hocus Pocus, we don't actually see Thackeray Binks' transformation into a cat, but we can hear his body changing shape, as well as the poor guy screaming as it happens. It doesn't sound comfortable at all.
In the 2010 remake of The Wolfman 2010, turning into a werewolf involves a lot of snapping bones and blood from the mouth.
Averted in the original 1941 version, where the most painful thing was probably the actor having to sit still long enough for the lap dissolves to be recorded.
In The Avengers, the Hulk's first transformation looks excruciating and takes a long time, because Banner is fighting it the whole time. The second time, he transforms intentionally and it only takes one smooth second, with no thrashing or screaming.
The first time Dr. Curt Connors changes into the Lizard in The Amazing Spider-Man, he is not having a good time.
Both situations happen in Animorphs: the actual physical transformation can be rather disturbing unless the character has the knack for it (Cassie does), and upon first transforming, the instincts of the animal take over temporarily. It's implied that it should be considerably more painful, physically, but that the alien Applied Phlebotinum numbs it.
Also, something of a self-conscious aversion: morphing is explicitly painless, but looks and feels like it should hurt. In some ways, this is even creepier than just agonizing pain. In one book it was compared to having dental surgery with Novocain: it doesn't hurt, but you know it should, so that just makes it worse.
Werewolf transformations are described as being excruciatingly painful. Animagi amd Metamorphmagi, however, easily transform at will without the slightest discomfort.
The same series also features the Polyjuice Potion, whose transformation description includes the phrase bubbling skin... creepy and painful.
A more mundane version exists when characters have to drink skelegrow as a result of regrowing lost skeletal parts (Harry had to do so thanks to a botched attempt at mending Harry's arm when his arm was broken during a Quidditch match), and it is stated that the process is extremely painful and would require the entire night at the infirmary.
A gradual version in Keys to the Kingdom: as Arthur's flesh and blood become more saturated with magic, he is shown to scream in agony as his bones and muscles shift and grow to make him taller, more handsome, and "more perfect".
The Strange Case of Dr. Jekyll and Mr. Hyde: When Dr. Jekyll drank his potion, "the most racking pangs succeeded: a grinding in the bones, deadly nausea, and a horror of the spirit that cannot be exceeded at the hour of birth or death."
Inferno XXIV of The Divine Comedy gives a vivid account of shades transforming into snakes, and vice versa.
Dr. Franklin's Island by Ann Halam, two girls get turned into a fish and a bird. The narrator describes this as being really uncomfortable. The bird-girl's sternum goes clean through the skin of her chest, not a pretty picture.
The transformation back is over in almost one day and completely painless.
In Gaunt's Ghosts, the rogue Inquisitor Handro Rime has a collection of agents known collectively as the Sirkle. They all share the same face, to act as doubles for the Inquisitor, and it is implied the two scenes that he dies in are in fact his doubles. It's revealed that they use a special form of internal mechanism to alter the tension and position of muscles and even fracture and reset bone. It is repeatedly noted that it is incredibly, requires immense focus to maintain one face, and a moment of surprise causes them to reveal their true face. And that when ever they transform, it occurs with a horrifying crunch of bone. Cue Hero Killer moments.
Werewolves in The Parasol Protectorate face this problem when shifting between human and wolf forms. The physical pain never lessens, but older wolves get better at hiding it, culminating in Professor Lyall who is the most graceful shifter anyone in the cast has ever seen. The initial metamorphosis is also generally painful, but only because it normally involves an Alpha werewolf tearing you a new one.
The regeneration process experienced by Time Lords is, if not always physically painful, an extremely traumatic and draining experience. Typically, just after regenerating the Doctor finds himself weakened, partially amnesiac, and, in a few cases, comatose.
The Master's regeneration in "Utopia" shows him screaming throughout the whole process. Extra creepy when his face morphs and the scream pitches up.
The Doctor's forced aging in "The Sound of Drums" and again in "Last of the Time Lords" certainly sounds painful, judging by the screaming.
When the Doctor becomes (temporarily) human the process is only seen during a few extremely brief flashbacks—and he's screaming in anguish the entire time.
When the Eleventh Doctor shows up in The Sarah Jane Adventures, Sarah asks him if it hurt the last time changed. "It always hurts," is his reply.
Heroes: When Mohinder injects himself with an experimental serum trying to give himself an ability, his ability at first includes super strength and agility. However, he slowly starts to transform into a monster of sorts and there is visible pain and discomfort that accompanies the transformation.
George's werewolf transformation is, if the way he screams is any indication, agony. During the transformation, a werewolf has every organ in his body simultaneously stop: heart attack, kidney failure, liver failure, and so on. Meanwhile his bones are cracking and twisting against each other, and his skin and muscles are being brutally torn apart. He screams at first, until the change hits the throat and vocal chords. Normally a human in pain has defenses, such hormones that dull pain receptors, but those systems are gone too, leaving absolutely nothing to help with the pain.
Nina: It looks so painful. What happens to you, what does it feel like?
George: There aren't words.
It's implied that when a person dies, they go to an unknown place where terrifying things happen to them. So when a person comes back as a vampire or ghost, they haven't had the best time.
Werewolves get the really bad end of the stick on The Vampire Diaries; it takes over five hours of horrible pain before there's even any visible changes. Though at least that part does get shorter over time.
The transformation to vampire in True Blood has been described as incredibly painful and horrifying by vampire protagonist Bill, who had vowed never to turn another human into a vampire to ensure that nobody else has to experience what he went through.
Supernatural: Shapeshifters have to go through this every time they switch forms, with teeth falling out, internal things rearranging with many a crunching, squelching sound, and finally having to peel their own skin off. Made more jarring and squicky because the first time we see it, the shapeshifter looks like one of the main characters.
Zig-zagged with werewolves in Buffy the Vampire Slayer. The pain they go through when transforming varies. When Oz transforms from human to werewolf in season 2, the pain is incapacitating: he doubles over, tries to get away but falls over, followed by restrained moaning. Transforming back, however, doesn't even wake him up. In season 3, he's perfectly quiet during all transformations, while in season 4, the time leading up to nightfall is described as "blood boiling". But Veruca enjoys it. Then in season 8, a group of werewolves is seen screaming and even coughing up blood, while Bay changes without a hitch.
Possibly justified when taking into account how much a werewolf wants to transform. Oz was quiet when he was safe and behind bars; Veruca loves being a werewolf; and Bay transformed out of protection. Characters who experience pain, however, always seem to fight it.
Jarbilong in Priest uses the body of a former vicar to take physical form in his battle against Ivan Isaacs. The poor sod screams a lot while his ribs stretch out of his chest and a new head grows out of his back.
Some versions of legend about werewolves actually either invert or subvert this trope, saying that while the transformation may appear to be excruciatingly painful, in truth it turns out to be sinfully pleasurable instead.
Mage: The Awakening features a spell whereby one can force a person to transform by forcing their new form to claw its way out of their normal body.
Infernal Exalted have the Charm Inner Devils Unchained, which turns the target into a demon. Painfully.
Then there's the process of becoming akuma, which throws in plenty of Mind Rape in addition to everything else.
Dungeons & Dragons v.3 has a sourcebook which expands on the rules and abilites of wizards and sorcerors called 'Tome and Blood'. It gives the Prestige Class of 'The Acolyte of the Skin', which is gained by summoning the essence of a fiend and binding it to your flesh. The illustration is not pretty.
The Ritual of Bonding is painful and not to be undertaken lightly. The ritual requires 10 rounds from initiation to completion, and once begun, nothing can halt its progress. The fiendish essence subsumes the caster's own skin, an agonizing process that deals 1d4 points of damage each round of the ritual—wise candidates keep some cure potions handy.
According to many sources about the Nine Hells of Baator, while any type of promotion among devils is painful, the promotion to pit fiend (one of the leaders of the race) is the worst. For this to happen, a devil must spend 999 days in the Pit of Flame on the fourth layer of Baator. The Pit of Flame is usually used to punish devils, contains fire so hot that even they find it agonizing, and is considered one of the worst punishments that an insubordinate can receive. In other words, surviving three years of it is the perfect test for one who wants to join the ruling class of Hell.
For the first half of the game Shadow Hearts, Yuri Hyuga convulses and screams when using his "Fusion" ability to combine with demons; whether the pain is mental or physical is unknown, but the former is implied. Partway through the game, he experiences an epiphany, whereupon he no longer suffers the Freak Out on using his power.
The sequel repeats this pattern, with another epiphany.
Midna's first transformation with the Fused Shadows in Twilight Princess had her being thrown around and screaming painfully.
The Parasite Eve series has a handful these transformations to emphasize just how unnatural the game's monsters are; in the first game, the first actual non-boss encounter is a rat which is put through a thoroughly traumatic transmutation; later on, a poor German Shepherd is given the same treatment. Not recommended for the weak of stomach.
Every monster in the Resident Evil series that is depicted transforming does so in a terrifying, disgusting, and obviously agonizing manner. Humans that transform have it worse, as the ones that scream don't bear thinking about.
Just about every transformation sequence with Sonic turning into the Werehog in Sonic Unleashed looks kinda painful for Sonic. However, transforming back to his normal self is almost instantaneous and looks completely painless, with Sonic looking relieved and content afterward. There's a nice touch in that every time you change the time of day while in the Next-Gen version's hub worlds (Either via Pause Menu or with hourglasses) it plays the appropriate transformation sequence as a Loading Screen.
In Diablo II, the Dark Wanderer assumes Diablo's true form in the cinematic between Acts 3 and 4. Lumps move under his skin, horns sprout from his brow, and his face stretches and twists as he howls in pain. Thankfully, he collapses and the rest of the transformation occurs hidden under his cloak.
In Folklore, Keats Transcended form basically has him beefing up and changing skin and hair colors. And from the way he screams and writhes around every time you activate it, it's rather unpleasant for him.
In Quake IV, the player character gets "Stroggified" into one of the enemy zombie-cyborgs, but is rescued before brainwashing and becomes a Phlebotinum Rebel. The Stroggification involves getting his legs cut off on a Conveyor Belt-O-Doom. Made all the worse by the player still having some control during the transformation but are unable to free them, as well as having to see (and especially hear) one the fellow Marines undergo the treatment first.
In Mega Man Zero 4: Dr. Weil, when undergoing his final transformation, has tubes being jammed into him (with copious amounts of blood in the Japanese version), and shouting something that roughly translates from Japanese as either "Can you see this Pain?! You'll never understand any of it?!" or "Can you understand pain such as this?!". The drama tapes even include him screaming and grunting in pain as he transforms in such a way that could be considered Nightmare Fuel.
Jak being forced into his dark form in Jak and Daxter, either by the Oracle or due to an overexposure of Dark Eco. The way he jerks and spasms as The Corruption takes over makes clear it's no picnic. Reverting back, though rather quickly, will have him grabbing his head and shuddering violently. In TLF it's implied that due to the massive amounts of Dark Eco present, even changing voluntarily will cause him so much pain that it will kill him.
Downplayed with Daxter's change from human to ottsel. "Man, that stung!"
killer 7 features Heaven Smiles as its regular enemies. While some of them are transformed humans, you rarely see the transformations. When you do, they usualy feature an instantaneous transformation or an ofscreen one. THEN we have Andrei Ulmeyda, whose transformation goes like this: The army, wishing to experiment on him to try and use Smiles as their own weapons, injects potent Heaven Smile tumors into him. The army triggers a small explosion for some reason, but then an even larger explosion occurs amd Ulmeyda asks why you didn't kill him at the injection and saying he "can't control this urge to kill." He then screams, his head then flies of his head, his acidic blood (acidic because of all the diseases he infected himself with to create vaccines) kills everyone in the army present, then his blood BRINGS HIS HEAD BACK ONTO HIS BODY AND PULLS UP HIS AFRO. Needless to say, Ulmeyda was in GREAT PAIN in his last moments of sanity.
When Rick puts on the Terror Mask for the first time in the Splatterhouse remake, it effectively destroys and remakes his muscular structure. He's in agony the entire time, and his flesh tears apart in the process. In fact, it causes so much damage to him that after A Taste of Power, the Terror Mask has to turn it down out of risk of killing him.
This is a problem for chimera in El Goonish Shive; it figures prominently in the character of Vlad, who could not change form with risking his life. Part of what makes Grace (Shade Tail) unique is that transforming doesn't hurt her as much as it does others (by design, she naturally releases painkillers when transforming). Interestingly, the transformation gun doesn't have this effect, even on normal humans (though it is implied that it did before Tedd perfected it; when Elliot uses the transformation belt, which is based on an earlier version of the TFG, he is incapacitated for several minutes - and his later cat-hybrid transformations reflect this as well). "Ok, I need an aspirin, a ball of yarn, and thirty-seven pounds of catnip, stat!"
Ariel from Drowtales has this as a natural limit on her hereditary shapeshifting power. It is strongly implied that changing her bodily structure too fast or too severely causes pain akin to a person with braces having their wires over-tightened, and she's specifically warned that if she's not careful she could shift a vital organ to the wrong place and potentially seriously injure or kill herself. She gets around the problem by primarily shapeshifting her hair, which of course has no nerve endings.
Most of Beast Boy's transformations on Teen Titans appear painless, except for the episode when an accidental shower of chemicals caused him to morph into a Hulk-like werebeast against his will. Also, Red Star, from the episode "Snowblind", definitely has this problem.
The 2006 revival of Biker Mice from Mars has Stoker change into a rat-like beast called Stoker Rat when under sunlight. The transformation first occurred in the episode "Changes" and happened again in "British Invasion." The transformation is an ode to the transformation scene from An American Werewolf in London.
Demona's twice daily shifts between human and gargoyle on Gargoyles are shown to be very physically painful. Which is understandable, as she is gaining or losing several major limbs each time. The only consolation is that when her hated and mystically linked enemy, Macbeth, is in close range, he feels every bit of that pain because of their immortality connection.
If one of the eponymous Transformers hasn't transformed in an exceedingly long time, or is banged up badly enough, transforming can hurt like hell, or, in extreme cases, be fatal.
When Waspinator is put into Blackarachnia's transwarp machine in Transformers Animated, he screams and his hands can be seen clawing at the machine. Blackarachnia casually comments that it might hurt a bit.
Most upgrades the Transformers experience in Beast Wars seem to come off this way. Everyone's transition to Transmetal in the season 2 premier was accompanied by screams and bodies collapsing. The changes to Transmetal 2 seemed even worse.
In the Sponge Bob Square Pants episode "Mermaid Man and Barnacle Boy IV", Spongebob accidentally puts Designated Victim Squidward through a series of increasingly painful and graphic transformations (burning, being cut in half, being skinless, and some that were so grotesque they were only heard offscreen as sound effects that don't bear thinking about) while trying to undo the effects of a "small ray".
Danny Phantom actually has five instances, all Danny. The first and last sets of two are all seen as excrutiating agony. The middle one is Nightmare Fuel and what follows is just as disturbing and really should have earned a higher rating.
Ben's final stage of transformation into Benwolf, in Ben 10. For most of the episode, he'd just been gradually getting furry and wolflike, then... ouch.
In Street Sharks, getting turned into a mutant always involves a good bit of screaming. Makes sense, considering that occasional extra limbs are grown and all of them gain a good amount of extra muscle mass.
The Avengers endure some painful transformations in the Earth's Mightiest Heroes episode "Gamma World", as part of The Leader's plan to turn everyone in the world into Gamma-irritated monsters. Iron Man's pain receives particular emphasis, as the animators show the toll the gamma blast takes on his shrapnel-embedded heart.
Simon Williams' transformation into Wonder Man, in another episode, seems unbearable as well. The other characters mention that Simon became the only person to survive the process.