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 later meets other Shinigami who, through a slightly different process, ended up in basically 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.
One of The Hunter duo from Venus Versus Virus is a young girl who is an "Anti-Virus," a biological evolution against The Heartless monsters that plague mankind. However, this has resulted in a Split Personality that merely kills The Heartless first, and then turns on her partner. The Flash Forward at the beginning of the first episode implies that her two halves will become whole... but as a Face Heel Turn.
Naruto has several of these, in the form of the "Jinchuuruki". Naruto and Gaara are two; another is shown in the manga and others are implied to exist.
Actually not all of the Jinchuuruki count: Killer Bee and the Eight Tails seem to have a mutually beneficial relationship.
As it turns out, Killer Bee actually had to remove his dark side to gain control of the Hachibi. So he originally had one of these too, but got rid of it.
Major parts of the plot revolves around Naruto's struggle with the Kyuubi. At first, he benefits from the Kyuubi's power by simply asking for it. However, after the Time Skip, Naruto's usage of the Kyuubi is mainly out of rage. Naruto attempts to regain control after finding out that he near-fatally injured Jiraiya and attacked Sakura in his 4-tailed state, when Naruto is emotionally unconscious and the chakra takes over his body.
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.
Guts from Berserk - on occasion, when he enters the eponymous Unstoppable Rage, we see a hideous black houndlike entity hovering around him. Certain characters refer to it as the Beast, and it's hinted that his humanity will be lost to it if things keep going as they currently are.
There's a lot of debate in the Digimon Adventure 02 fandom as to the true nature of Ken Ichijoji's Digimon Kaiser personality - how much of it was his own doings and how much of it was a result of the Dark Spore? Alternate Character Interpretation suggests that it was a Split Personality (which isn't entirely illogical when you consider how different the Kaiser and regular Ken were) but it's more suggested that Ken is an example of how even the nicest person alive can turn nasty, making him more Enemy Within.
(Hell, these characters are all practically an allegory for modern digital relationships on the internet. So... yeah.)
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 similar to Inuyasha above actually.
In D. Gray-Man, it's revealed that the 14th Noah wants to kill The Millennium Earl so he can become the next Millennium Earl. His host, on the other hand, would rather not.
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.
Haine of DOGS Bullets And 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 his childhood friend, and also another experiment, Lily. Arguably, all characters who have a Cerberus spine fall under this trope.
The eponymous character of Soul Eater deals with this, especially as it pertains to keeping Maka safe. He literally 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.
Comic Books
Marvel's 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. Of course, 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 of the Hulk'smany personalities, the Devil Hulk, is a cold-blooded monster that seeks to destroy everything Bruce Banner holds dear. Fortunately for the Marvel Universe, Banner and the other Hulk personalities have managed to keep it imprisoned in Banner's psyche.
One timeline in the Marvel continuity of 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.
Shade and Trent, the serial killer whose body Shade inhabited, were both the others' Enemy Within. Trent tried to take back control by releasing even more enemies within, but it turned out Shade had enough of those to outnumber him.
Green Lantern Hal Jordan died inside the sun to save the world after becoming / being possessed by the fear entity Parallax; he later reappeared as the latest spiritual host of Justice entity The Spectre, and then before he was ultimately resurrected good as new there was a terrible period where Jordan, Parallax, and the Spectre were all fighting for control in ways that eventually visually warped him.
Werewolves in any story in which the werewolf form is disconnected from, or uncontrollable by, the human form. Sympathetic folktales about otherwise good people suffering from lycanthropy help make this trope Older Than Print.
Literature
Rand al'Thor and Lews Therin in Robert Jordan's 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 literally 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.
Although this was somewhat more metaphorical, rather than an actual separate entity like some other cases listed on this page. Or at least until Thud! came around and the Summoning Dark attempted to hijack it and turn Vimes into an agent of pure spite-driven vengeance. It was driven out by the rigid self-control mentioned above however, personified as Vimes' "Inner Watchman." Who watches the Watchmen? This guy.
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 Scheckley. 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.
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.
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.
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. Of course, 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.
In the Doctor Who episode "Amy's Choice", the Doctor, Amy and Rory find themselves trapped by the "Dream Lord", who forces them to choose between two separate realities. When they awaken, the Doctor reveals that the "Dream Lord" was patterned after his own darker side.
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.
To emphasize this, Imperial propaganda reminds you that "For every enemy withoutthere are a hundred within". Of course, they're talking about the Imperium itself, but what that means is that it's teeming with heretics, so many that they outnumber those actually loyal to the Emperor a billion to one. I suppose that means that the those higher up on the totem pole think that the average Imperial subject failed math (which wouldn't be surprising). Regardless of how much it's emphasized, there's a bit a truth to it: Warhammer 40,000 has enemies within in spades, and all too often the enemy within wins.
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 addition to Vampire, there's also Wraith. The Shadow of a Wraith is essentially "the Beast" on steroids. It's self-aware, manipulative, can contact its buddies and has the goal of either taking over the Wraith's corpus or driving it into Oblivion, the Final Death.
The Kuei-jin, the Asian vampires, don't have a Beast. They have a P'o, which is to all intents and purposes one of Wraith's Shadows.
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.
Infernal Exalted have the Unwoven Coadjutor, a demon that lives inside their soul. The Infernals' reactions to this range from "awesome, demon buddy!" to "JUST SHUT UP!", especially since the coadjutor is responsible for their Torment track that punishes them for not serving the Yozis. (With the Broken-Winged Crane release, there are Charms specifically allowing them to break the coadjutor's influence.)
They get this twice over-a Green Sun Prince's Exaltation often has memories from its last Solar bearer that are so complete, they recreate the personality of said Solar. This is not a good thing.
Video Games
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, has 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. We later find out that Emil is really being possessed by Ratatosk, the sentient-life-hating deity, that the supposed antagonist Richter has been trying to kill all along.
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 The Prince of Persia: The Two Thrones, the "Dark Prince" initially acts like a benign Exposition Fairy, seeming to be just like the prince, only with fewer scruples. Strangely enough for this trope, he never makes an actual bid for control over the Prince's body until the very end, spending most of his time trying to corrupt the Prince—though 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. Of course, 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 Personae (of the Persona RPG series) are supernatural spirits that exist within a person's psyche, representing their unconscious selves. Hence, the more nasty Personae tend to have unpleasant effects on their host...
In Persona, Guido's Persona ends up taking over his body.
To elaborate, these last two examples may not really count... because both involve hardcore Mind Rape and Body Horror inflicted by Nyarlathotep rather than any true actual enemy withins. He's the reflection of all evil in Humanity's spirit, hence, he can force the darkest facets of any given human to emerge when they allow themselves to fall into his control.
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.
In the eroge strategy game Sengoku Rance, Nobunaga is possessed by the demon known as Xaiver, after he acidentally breaks one of the eight gourds containing Xaiver's essence.
In Sly Cooper 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.
Visual Novels
Shiki of Tsukihime suffers from this in a ridiculous number of ways. In some routes, he dreams that he's brutally killing people and drinking their blood, only to find out the next day that the murders really happened, fueling fears that he himself is a monster (he only has a link to the actual killer, though). In one route, the Big Bad's soul really is starting to possess him, carrying over its vampiric attributes and desires. In all the routes, however, he sometimes feels inexplicable homicidal urges that drive him to eliminate those around him, sometimes completely overpowering him and taking over as a distinct persona with an entirely different mindset.
In the dream-world of the side story, Kagetsu Tohya, Shiki's amoral split personality, Nanaya Shiki, actually gains a form of its own and tries to permanently take over his body.
In this case, Shiki has two "Enemies Within." There is SHIKI/Roa, an entirely different person who is linked to him due to "the incident." Then there is "Nanaya Shiki," who truly is another side of him, with a twist - despite barely appearing, he's the original personality, the Shiki who would have been had his clan not been wiped out during his childhood and him later brainwashed to be Tohno Shiki.
In Remember11, Kokoro and Satoru switch minds, sometimes causing trouble when the two appear to have mutually-exclusive priorities. Most of the trouble is actually caused by a third personality that had been taking over their minds, which the two of them never noticed due to poor communication
Web Comics
In Girl Genius, Agatha gets taken over by The Other (Big Bad of the story, who may or may not be her mother Lucrezia Mongfish.) They struggle for control of her body until The Other unwittingly puts on a locket that keeps Agatha in control.
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.
Web Original
Yoi, of Magical Girl Hunters has his split personality Koi who eventually gains his own body.
Kickassia implies that Dr. Insano used to be this to Spoony, who eventually won a hard-fought battle for control, turning them into Jekyll and Hyde.
Hafidha and her Bug in Shadow Unit, and by extension, all the gammas, are along these lines. Made worse by the fact that the Anomaly isn't necessarily always in control of the host.
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 Transformers Energon, Megatron/Galvatron thinks he is controlling Unicron as a superweapon. However, it becomes increasingly clear that Unicron is the one subtly controlling him. After Unicron's body is destroyed (yes, again), it becomes a bit more overt and Unicron actually "talks" inside his head, although he doesn't realize it's another person until it's almost too late.
In Gargoyles, Coldstone is created with the dead bodies and souls of three different gargoyles. Two of those gargoyles are were Happily Married, and the third is was determined to break up their marriage and kill Goliath.
