Ichigo from Bleach regained tremendous Shinigami powers, but the method he used resulted in the awakening of a dark personality, an "Inner Hollow" within his consciousness. Throughout the series a recurring theme is having to battle this inner demon for control of his powers made stronger by their dual existence. Ichigo gains even greater power when he finally accepts that his Inner Hollow isn't an enemy but just another part of him.
Ichigo later meets other Shinigami who, through a slightly different process, ended up in the same situation. They trained him in how to properly overcome and control his inner demon, but he ended up leaving before the training was complete.
There's also a variant with Alice, who split into Dark and White Alice, upon fusing with an alien lifeform. While Dark Alice isn't within White Alice, she does represent her dark desires and hatred for humanity, and White Alice is shown to be horrified by her actions, but almost completely helpless to stop them.
Inuyasha has this in the form of his demon blood. Being a half demon, half human, his demon blood is considered too powerful for him to control. When it takes control, it turns him into a mindless animal that attacks purely on instinct, unable to tell friend from foe. Inuyasha's father gave him a safeguard in the form of his Empathic Weapon Tessaiga to keep it in check. As long as the sword remains in Inuyasha's possession, his demon side is suppressed, though he remains stronger than the average human for it.
Senri from +Anima has an eyepatch in order to keep his +Anima in check, without it he goes berserk.
In Dragon Ball Z, Majin Buu was introduced as a huge, pink, disturbingly cheerful jinn that liked to turn people into candy and eat them. However, an encounter with an injured dog and Hercule/Mr. Satan caused a Heel-Face Turn. Crisis averted, right? Well, up until the dog gets shot, at which point he becomes so furious that all of his inner evil comes to life. It then eats him, becoming even more powerful than the original as a result. Becomes inverted when the good part of Buu struggles inside of himself in a desperate attempt to save Hercule/Mr. Satan, becoming the Ally Within you could say.
Haine of Dogs: Bullets & Carnage has one in the form of a 'mad dog' due to the experimentation he suffered as a child. It overtly led to the the death of Lily, his childhood friend and fellow experimental subject.
The eponymous character of Soul Eater deals with this, especially as it pertains to keeping Maka safe. He has a small ogre-demon living inside his soul. It starts to take over in the final battle with Asura (in the anime), when Maka has to go into Soul's soul and save the real Soul from the ogre-demon, who has disguised himself to look exactly like the guy, in order to save her partner from the Madness with the Power of Love.
Rogue from Fairy Tail will occasionally hear a voice from his shadow encouraging him, if not outright forcing him, to do wrong. According to his future self the shadow is the manifestation of any darkness in Rogue's heart, and will never completely leave him alone.
All of the Claymores deal with this. While they can enhance their strength and speed by getting in touch with their Yoma side, they also place their humanity at risk. Most can control their dark side, but others submit to it and turn on their friends and the human race.
Marvel's The Sentry character housed a dark and equally powerful villain known as the Void. In his original appearances, the Void manifested as a seperate entity outside of the Sentry's body. In later appearances, the Sentry transformed into the Void. The most recent depictions show the Sentry retaining his human appearance, while his eyes turn black. In the Sentry's final battle, he is possessed by the Void. When his body is punctured, black tentacles issue from the wound.
Malus Darkblade and T'zarkan in the Malus Darkblade series. Malus is already a very evil person and as such doesn't exactly need goading, but T'zarkan tempts him with power at the cost of more of his soul.
One timeline in the Marvel continuity of The Transformers comic books had Rodimus Prime trapping Unicron inside the Matrix...which was located in Rodimus' chest. It wasn't pretty when Unicron managed to break free and posses the young Prime's body.
An issue of the French comic book Nävis features Girodouss, an alien who takes on a monstrous alterego when she gets hungry and doesn't change back until she's hunted down and devoured her prey. This is normal for her species, but Girodouss doesn't like to kill. She can only be cured of this by mating, but in doing so, she will go into one final rage and murder her mate. Fortunately, she's able to Take a Third Option.
Parodied in Blue Beetle. Eclipso turns Blue Beetle into his deepest, darkest power fantasy, hoping to get an ally out of the deal. Unfortunately for her, Blue Beetle is an example of Incorruptible Pure Pureness, so he becomes a dentist. And a pretty nice one, at that. "Hey dentists make six figures a year!"
Loneliness, the first Big Bad of the Pony POV Series, is this to Trixie, keeping her practically comatose for weeks even after Discord's defeat until Twilight enters Trixie's mind and helps Trixie defeat her. What's truly terrifying about her is that it's never made clear exactly what she is or where she came from.
Fluttercruel was originally an ineffective one of these, being more a mild annoyance to Fluttershy than anything else, and even when she finally manages to take control of Fluttershy's body, all she does is party, rather than anything evil... though her actions do accidentally lead to Fluttershy becoming Nightmare Whisper. But that just makes her have a Heel-Face Turn, and she and Fluttershy now share a body and get along very well (they both consider Cruel to be Shy's "daughter").
Stairway To Equestria: Similarly to Luna, Midnight Blink has in inner Nightmare of his own that he has to deal with constantly throughout part two and three of the story.
Kali with Kira in the Death Note fanfic "Zenith, Darkness, Reverie". If Kali has a callous disregard for human existence, Kira is this, with a penchant for murder and determination to assert control of Kali's body to do so. Kira also considers Kali's emotions to be a "vulnerability", despite her relatively obvious lack of sentimentality. This is Kira's primary justification for killing the protagonist. Unfortunately, Kali is not as expendable as Kira would prefer.
Inner Demons: The plot is driven by Twilight's dark side awakening and eventually consuming her mind, making her become the foretold Queen of Darkness. Becomes an Enemy Without during the Final Battle, when the Elements of Harmony force the Darkness out of Twilight's body, causing it to take on a form of its own.
Kage: Jade's Queen of the Shadowkhan persona, reawakened by Drago's spell, is working to corrupt her and eventually assume control completely. In the meantime, she's spending her time snarking at Jade whenever she can.
The Lion King Adventures: Twice, Simba is faced with mental battles with the King of Dreams, the embodiment of his dark side. Ultimately, he's defeated for good when Simba decides to embrace and control his dark side, denying the King any power and destroying him.
Older Than Print: Werewolves in any story in which the werewolf form is disconnected from, or uncontrollable by, the human form. There are sympathetic folktales about otherwise good people suffering from lycanthropy.
White Court Vampires in The Dresden Files. It's called their Demon and their Hunger, and only Thomas even tries to fight it. It exerts control especially in the presence of the relevant emotional "food", though if the vampire tries to starve it out they go mad with Hunger and mindlessly try to Feed. It can be killed if the host experiences the true emotion related to their feeding - love vs lust, etc.
Red Court Vampires have a similar deal. Theirs physically transforms them once they feed the first time, but until then they have a bloodlust.
Fallen Angels - the Order of the Blackened Denarius - do this to gain the cooperation of (and control over) their hosts. Lasciel in particular is known for being especially good at this.
The Mantle of the Winter Knight is this for its host.
Rand al'Thor and Lews Therin Telamon in Robert Jordan's The Wheel of Time series. It's never made certain whether Lews Therin really does exist, or whether Rand is simply becoming insane due to the taint on Saidin and pure stress. In the eleventh book, Semirhage reveals that those who hear the voices of previous incarnations are doomed to go mad anyway and is in fact worse as, unlike with merely insane people, there is little hope of recovery because the voices are real after all.
Given the number of things he could not know unless the voice in his head really is Lews Therin, it's pretty certain. It also shows up long before he develops any of his other Taint-related symptoms.
It is now confirmed that Rand had access to Lews Therin's memories because he is his reincarnation, but the actual Lews Therin "voice" was just a symptom of his madness and identity issues. He appears to have sorted that out with a Split Personality Merge as of the end of the 12th book.
Dandra in The Dragon Below trilogy has a rather complicated version in the form of the imprisoned personality of her creator, Tetkashtai.
Nearra in the first six books of Dragonlance: The New Adventures has one.
In Orson Scott Card's The Devil in Velvet, the protagonist, Nicholas, makes a deal with the Devil to return in time to 18th century England to stop a murder most foul by, in essence, leaping INTO and taking over control of the body of his ancient ancestor. But the old boy is still there, trying to get out of the box, and whenever Nicholas is extremely stressed or emotional, Old Nick jumps out, seizes control of his body, and does dastardly things until our hero can regain control.
Granny Weatherwax (the Discworld's greatest witch) is also hinted to have a much darker side which she keeps in check with her insistence on doing what is Right. After she's bitten by a vampire in Carpe Jugulum, she faces down this dark side in a sort of Battle in the Center of the Mind.
In Return of the Archwizards Galaeron Nihmedu overused the shadow magic despite his mentor's warning. This puts him into the "shadow crisis" — that is, now his "shadow self" got a foothold in him and it sucks to be Galaeron very much, in several ways at once. May be the best reply (and counterpart) to Enemy Without of Earthsea Trilogy ever.
"The Status Civilization" by Robert Sheckley. The protagonist is exiled to the planet of criminals as a convicted murderer. He doesn't believe he could have killed in cold blood but has to kill in self-defense in exile. In the end, he finds out the truth: he was framed for a murder and he turned himself in because his subconcious considered him guilty and everyone on the Earth was Brain Washed to turn in themselves.
In Scorpion Shards, the protagonists are infected by otherworldly parasites that turn their superpowers to evil. Giving in to the corrupted, evil urges feeds the parasites.
There is a classic treatment in Julian May's Galactic Milieu Trilogy (Jack the Bodiless, Diamond Mask, Magnificat), where a principal adversary is an immaterial being called Fury that turns out to be a subconscious manifestation of a major character.
In the New Jedi Order series, after an attempt to brainwash her completely goes wrong, Tahiri ends up with one of these in the form of Yuuzhan Vong personality Riina Kwaad. Riina's not evil exactly, but she is very messed up and her attempts to pull a Split Personality Takeover do a serious number on both their sanities. They end up doing a Split Personality Merge instead.
The House of Night: Usually involves Red Vampyres and Red Fledglings about how having dark feelings doesn't make you a monster, acting out on them does.
Live Action TV
Supernatural's Sam Winchester is a sort of human/demon hybrid and constantly fights against his demonic inheritance, which includes a portion of natural arrogance, but under the right circumstances ( drinking enough "demon blood") turns him completely and murderously feral.
Considering what transpires in the 6th season's finale Soulless Sam likely counts as well.
Angel, and vampires with souls in general, from Buffy the Vampire Slayer and Angel. Buffyverse vampires are generally corpses of people without a soul, and thus a conscience; only the memories and intelligence of their former human selves keeps them from becoming completely feral. However, if a vampire regains their soul (as Angel did, and Spike eventually does), this trope comes into full effect: despite having a human soul again, their demonic nature is still present and has to constantly be kept in check.
Oz, to a lesser extent. His werewolf self isn't exactly bad, but wild and uncontrollable, and he certainly fears doing harm to someone during the full moon. He later gets Put on a Bus when he realizes that his werewolf side's beginning to affect his human personality, and sets off to find a cure.
Especially true in the case of Angel. Angelus hates being trapped in Angel since he has to deal with Angel's altruism, but takes comfort in the fact that he'll always be able to torment Angel.
Forever Knight has Nick Knight, a vampire trying to earn redemption as a Toronto homocide detective, struggling to suppress his predatory nature and bloodlust. Unlike the vampires in Buffy and Angel, vampires in Forever Knight do generally have souls: most of them just give in to their new instincts fairly quickly and never look back.
Played with in Kamen Rider Den-O. Because the main character and his Anti-Hero rival are special individuals called Singularity Points, they can exert their will when Imagin possess them. While most Imagin are brash monsters, those bonded with the heroes are considerably mellower and end up befriending their human partners, making this more an example of Ally Within.
Played a bit straighter with Ryutaros, who due to being buried deep within Ryotaro's psyche for an extended period of time, is much harder to drive out. That, combined with his willful and childish nature, can sometimes cause major problems, as seen in one episode where he decided to beat the Monster of the Week by killing the human to whom it was bonded. At the end of the day, though, he's still an ally.
Hyde from Jekyll. Though he eventually stops being an enemy.
Crichton when possessed by the Scorpius neural clone in Farscape.
CSI: Crime Scene Investigation had a metaphorical version of this with Ray Langston and his two season struggle against the dark streak he felt he had. The Unstoppable Rage variant is where it most likely fits. And it overtook him by the end of season 11 when he killed Nate Haskell after Haskell tormented him and kidnapped his ex-wife.
There is an episode of the original Star Trek that has almost the exact same title as this trope. (The Enemy Within) in which a transporter malfunction splits captain Kirk into a good/passive and an evil/aggressive version of him.
In an episode of Star Trek: Voyager, the Doctor tries to expand his program by incorporating personality aspects of various historical figures who possessed great minds. He failed to realize that he would also incorporate the darker sides of their psyches, and develops an evil split personality who takes Kes hostage.
Certain factions requires their members to conquer their enemy inside for them to join fully. The Space Wolves initiation rites have a phase in which you must conquer and learn to manage to maintain your beast within, or you'll turn into a Wulfen, a werewolf-like being. And not even once you have managed to pass this stage, it is not sure whether or not the curse is truly gone. Already initiated members can have the curse activate in the middle of the battlefield, and gain strength beyond even their already superhuman abilities. While this is usually temporary and the one affected will return to his normal form after the battle is over, this is the result of the curse not stabilizing completely during the initiation rites.
Eldar warriors must contain the curse of Khaine within them, learning to don and doff their 'war mask' on command, lest they be trapped upon the Path of the Warrior and become an Exarch, forever imprisoned within the armor of his predecessors, bound into the gestalt consciousness that is the Exarch, incapable of peace and unable to die.
Vampire: The Masquerade has a large bit of its mythos based around this - each Vampire is at least partially under the control of "The Beast," the representation of their Horror Hunger. The Beast is their id; it makes them feed, it makes them run from fire and oncoming sunlight, and it makes them Frenzy if they get scared or hungry enough.
The arc phrase of the game is actually "A beast I am, lest a Beast I become," which is an explicit statement that vampires are driven to do horrible things to control their inner hunger, and that trying to avoid doing those things will essentially lead to you losing control entirely and becoming little more than a mindless monster that does nothing but kill and feed like an animal. Try to be humane, try to be "good", and you'll ultimately become a far worse monster than people who are willing to kill and feed in moderation.
In D&D 4th Ed the Minotaurs have to struggle against releasing the beast within. So much that they adorn everything they wear and carry, and sometimes themselves with labyrinth designs to symbolize that struggle in their mind and soul.
In Kingdom Hearts, Rival Turned Evil Riku fuses with the villain from the first game. He redeems, but is struggling with the darkness within in the sequels.
Leo in Manhunt 2. He is a Split Personality that is planted by Dr. Danny Lamb in order to pay off his debts. However, it went wrong when the Pickman Bridge malfunctioned, resulting in Danny being able to see and talk to Leo as if he was a real person.
Emil, the main character from Tales of Symphonia Dawn of the New World, is a strange case. As it stands at the beginning, he has the original flavor: a bad case of multiple personality disorder, in which his usually meek self is replaced with a powerful, badass red-eyed alter-ego whenever he needs to fight. Later this side of him becomes increasingly dominant and much more of a jerk. While at first it appears it's a part of his contract with Ratatosk, we later find out that Emil is really being possessed by Ratatosk himself, the sentient-life-hating deity, that the supposed antagonist Richter has been trying to kill all along. But then comes the BIG twist: "Emil" really IS Ratatosk, amnesiac after being awakened improperly. In order to fill in the gaps in his memory, Ratatosk created a new personality for himself, styling his appearance after Richter's best friend Aster, whose murder started the whole debacle, and taking the name "Emil" from a random dying woman in Palmacosta who didn't recognize him in her dying moments and mistook Ratatosk for her son. So the Split Personality Takeover in this case is the original persona reasserting dominance over the facade it had created.
The protagonist of Wild ARMs 2 fuses with a demon destined to destroy the world and because of this he can use the sword destined to defeat said demon...on other villains.
Both Leona & Iori from the King of Fighters series struggle with the curse of their bloodlines, which at times can cause them to regress into a berserker state know as "Riot of the Blood". Leona killed her entire family when she was in the Riot, and Iori has killed or severely wounded others as well.
In fact, it's implied that being able to resurface and take over your body has been part of his plan all along - a means of surviving beyond death, if his initial plan to defeat the evil had failed.
Akachi in Neverwinter Nights 2: Mask of the Betrayer forces you to continually consume other spirits or have your soul consumed instead. The main quest of the game is figuring out a way to get rid of the curse. The most extreme Evil ending actually involves you devouring Akachi's spirit itself to become a horrific, god-killing abomination.
In Prince of Persia: The Two Thrones, the Prince's arm is injured and subsequently corrupted by the Sands Of Time. As this taint slowly kills him his own darker personality begins to manifest as the "Dark Prince."
The Dark Prince initially acts like a benign Exposition Fairy, seeming to be just like the Prince, only with fewer scruples. Over the course of story the corruption caused by the sands grows worse and the instances of the darker personality coming to the surface more frequent. However whilst his outward appearance changes to that of the Dark Prince when overwhelmed by the sands taint, he retains enough control to seek out water to keep the curse at bay. Failing to reach water in time during these sequences causes him to die due to the corruption overwhelming him.
Strangely enough for this trope, he never makes an actual bid for control over the Prince's body until the very end. Instead spending most of his time trying to corrupt the Prince. Though until the Prince had managed to suppress the Dark Prince through willpower alone, he had little reason to vie for control as he was certain the corruption would kill him in due time. After the Prince rejects his help, he just petulantly taunts and distracts you during That One Level.
Condemned 2 has the Alcohol Demon, a manifestation of Ethan Thomas' alcoholism. At numerous occasions through the game, Ethan is tormented by the damn thing until he eventually "kills" it, in a bar no less. He was, however, trying to help you get yourself together. It doesn't die - it comes back a mission or two later, and points out it represents -all- his demons, not just alcohol.
The final boss in Castlevania: Aria of Sorrow is the embodiment of Dracula's evil, which threatens to possess and overwhelm Dracula's reincarnated self, Soma Cruz.
The Personas (of the Persona RPG series) are supernatural spirits that exist within a person's psyche, representing their unconscious selves. Hence, the more nasty Personas tend to have unpleasant effects on their host...
In Persona 3, the members of Strega have Personas that actively try to kill them. To prevent this, they have to take suppressants that have nasty side-effects. This is because their Personas were forcefully awakened.
The Shadows. They're manifestations of humanity's worst flaws and suppressed dark thoughts. It's best shown in Persona 4, in which the protagonists each have to face shadow versions of themselves. In this case, suppressing the Enemy Within is the worst possible course of action since this is what makes them hostile. Accepting their flaws and resolving to deal with them via character development transforms the Shadows into Personas.
In Sly 3: Honor Among Thieves, The Panda King (one of the villains of the first game) is trapped within his mind of his failure against Sly. Eventually Sly himself enters his mind to convince him into an Enemy Mine and snap out of the trance to save his daughter, who's captured by a local warlord.
A rather weird example played for laughs is found at the end of Fallout: New Vegas DLC Old World Blues, where you confront your very own Brain in a Jar, who is completely pissed off at you for the various wacky hijinks you've been getting into back in the Mojave at the expense of your body and hygiene. You then have to convince it to cooperate with you and if you want, rejoin your body.
A variation is used in Metal Gear Solid: Portable Ops. After the ICBMG is completed, Gene implies in his speech that there is a soldier under his employ that is ordered to kill them for their "betrayal." He then throws a knife at the unfortunate soldier that catches he eye, and the stabbing pain results in him firing his rifle at another soldier unwillingly. The soldiers then fire amongst themselves.
Ryu from Street Fighter is a Blood Knight but also surprisingly in control and an overall nice guy. Thing is, the art he learned gave way for a darker side of him that he has to keep in control. When the power activates, he's called Evil Ryu. It's still Ryu, but he's driven mad and doesn't hold back anything at all. He comes closer to being the next Akuma.
Pyramid Head from Silent Hill is the physical manifestation of James Sunderland's desire to be punished for murdering his wife.
In EarthBound, Ness's Nightmare is the manifestation of his inner demons within Ness's mind that holds back his full power. After Ness defeats it, his Psychic Powers expand rapidly.
Shiki Tohno of Tsukihime has one in the form of Shiki Nanaya. He is the embodiment of the bloodthirsty, sadistic killer that Shiki fears he could become (or would have become had his life gone a different direction). In fact, he's far too kindhearted to have ever wound up that way, but since when has fear been entirely rational?
In Disgaea 3, Dark Mao is Mao's pure evil essence embodied into a Heart Resident. Dark Mao was being secretly raised by Aurum during his time as Geoffrey to help turn Mao into the "Strongest Overlord".
In Girl Genius, Agatha gets taken over by "The Other" (who either was or previously possessed her mother Lucrezia Mongfish). They struggle for control of her body until The Other unwittingly puts on a locket that keeps Agatha in control. Since without the locker she emerges again, and it's not clear how much memories may cross-leak, this is treated as both turn-off for her suitors and a security problem.
Mr. Chalk from Zebra Girl, seems to be the manifestation of Sandra's demonic taint and appears in her dreams in order to drive her to cause pain and suffering. Amazingly, he's not the one that caused her Face-Heel Turn.
In TwoKinds Trace Legacy and his previous self, before losing his memories is one of these, though he's not actively fighting it... yet.
The Reveal behind the Big Bad in Animerica's second season is that he has a "demon side", being created from his constantly repressed negative thoughts on his twin Kasuse and the fear and sadness he felt from being The Unfavorite. The evil side constantly makes use of More than Mind Control to his good side, promising that Evil Feels Good and that he'll have a better life. However by Season 3 when the two converse once more Kiyone rejects his evil side, declaring that it only made his life worse and that he wants to atone for his sins. It is due to Ron's speech and his love for Yumi that he manages to overcome the demon within him.
It's implied that Beast Boy went through this as well with his Super-Beast form.
The two actually have a little chat about this at the end of the episode where Beast Boy got said form.
On a very similar show, season two of Legion of Super Heroes saw Brainiac 5 discover the power available by accessing evil Brainiac 1.0's memories. But then, well, this trope. He ends up playing super-chess in his head.
In Scooby-Doo! Mystery Incorporated, it turns out that association with the Nibiru entity inverts this trope by slowly sealing away someone's good side in a frozen extradimensional room. Hence Nibiru is responsible for all the other Complete Monsters in the show.