Ghost in the Machine

*Phone rings*
Jay: Hello?
Familiar Voice: Hello Jay, this is your inner child. I escaped and I just held up a liquor store! *sirens* Gotta go!

—The Critic

Cartesian philosophy includes a notion that there is, in effect, a little guy inside your head. He sits on your pineal gland and works the controls that make your robot-like body move around, much like the pilot of a Mobile Suit Human—that little guy is the "real you", and he's a much deeper and more interesting guy than the physical "you" that everyone else gets to see, mostly because the human body has lousy User Interface design. Some (though not all) schools of philosophy dismiss this notion, such as phenomonology and positivism (see Consciousness Explained by Daniel Dennett for an alleged thorough experimental demolition of the "Cartesian Theatre"; alternatively, see The Conscious Mind by David Chalmers for a theoretical defence of a similar idea).

In any event in the land of TV the notion of a ghost in the machine is not only philosophically dominant but also often literally true. Of course, this might cause Fridge Logic issues when one asks oneself whether this "little person" needs to have an even smaller person inside them, leading to an infinite regress. See the Homunculus Fallacy for more info on this theory.

Insert joke about TV writers being behind the times here if you like, but the idea remains dominant mostly because it makes such a good parallel to the experience of the viewer.

This is realized in numerous ways:

The Herman's Head notion: actual little people live inside your brain, each representing some aspect of your personality
Inner Monologue is, essentially, an expression of the character's "inner self" speaking about his actions as if he were a passive observer
Robo Cam is the application of this concept to robots: essentially, treating the robot as if it were a man in a robot suit.
Freaky Friday Flip is simply switching the little guys into different bodies. Not Himself or Puppeteer Parasite is usually something sinister replacing the little guy.
Battle in the Center of the Mind is when two or more little guys fight it out to see who's driving.
Journey to the Center of the Mind is when the cast goes to visit those little guys.

External manifestations, like the Good Angel, Bad Angel, are related.

Also seen in commercials for medicines and food items, where the little man has an acute need which only the advertiser's product can assuage, or is the malign cause thereof.

Anime and Manga

This happens on multiple occasions in My Next Life as a Villainess: All Routes Lead to Doom!.
In Neo-Human Casshern the human scientist Tetsuya Azuma needed to find a method where he could stand against BK-1 in combat, and so transferred his mind into the titular android.
Sayo of Mahou Sensei Negima is both a figurative AND literal example. For starters, she is an actual ghost possessing a tiny doll. This tiny doll pilots a Humongous Mecha, which is to say, a normal sized robot. Built to look like her.
On Bobobo-Bo Bo-bobo, little people who reflected Bobobo's state of mind would be seen inside or around Bobobo's head. Examples include two talking squirrels going through a break-up, the graduating class of a Japanese high school, a mecha pilot, and a rock band. The thing is, they were not only visible to the audience, but to the other characters.
Early episodes of Naruto had Sakura have an alter ego inside her head, an "Inner Sakura" who was easy to anger. This concept was dispensed with somewhat early on, however.
- Inner Sakura helped her shake off Ino's mind control since she was more stubborn than expected.
- Inner Sakura is more of a personification of what Sakura is really thinking. The gag was that whenever Sakura said something, Inner Sakura would be there to let the audience know what she really thought. Once Sakura became more assertive and outgoing, there was really no need for Inner Sakura.
A major part of the premise of Shugo Chara, where the Guardian Charas within everybody are their Ghost in the Machine brought out into the real world. Most people have one, but heroine Amu has three later four. That's one very busy machine.
An element of B Gata H Kei has everyone's sexual desires taking the form of small gods (or at least godlike) people that appear around their head.
In an early chapter of the Eyeshield 21 manga, Sena trying to remember how scoring extra points after a touch-down works is represented by an Imagine Spot of a mini-Sena running around a library before finally asking the Devil Bats' mascot about it. Sena even thinks to himself afterward "I've got quite a vivid imagination."
Ghost in the Shell: anime, manga, and OVA. Takes both a personal look at this, in everything from the mind of Motoko and the arc antagonists to the Case Of The Week, and the more Meta idea of consciousness born of the interactions of millions of consciousness. Most of the anime is spent looking into the idea of mind, consciousness and the viability of a reality in which virtual immersion is so consistently present. If you want to see this trope played with, subverted, deconstructed and reconstructed, this would be your primary base of examples. There are literally hundreds of individual examples to choose from, and all 3 mediums present probably the most thorough hypothetical analysis of the idea of the individual mind this side of the 21st century.
- Oh yeah, and the title is...well...relevant.

Comic Books

"The Numskulls", a strip which appeared in the British comic The Beezer (and later The Beano).
- "The Nervs" were a similar idea in Smash!
- In Leah Moore's Albion (which did to UK comics of the seventies what her father's League of Extraordinary Gentlemen did to Victorian literature), Numskulls and Nervs are both called "Menorgs", relating them to the rather odd theories of Alfred William Lawson.
  - Note that Numskulls and Nervs (and indeed Menorgs) don't just run the brain, they run the entire body. There's a Numskull in the mouth whose job is to shovel food down the hatch, and another whose job is to process it when it gets to the stomach.

Film

In Spy Kids 3: Game Over, the Toymaker creates three virtual representations of his ghosts; a hippy, a doctor and a soldier.
In the film version of Stephen King's Riding the Bullet, while Alan Parker is in the front seat of several vehicles, his inner self is in the back snarking all the way. His last driver, being dead and rather well-aware of the goings-on in the story, actually turns around and yells at Parker's inner-self to shut up already!
The film Osmosis Jones featured a less metaphysical version, showing a brain inhabited by technicians tapping away at computers which represented neurons.
In a segment of Woody Allen's Everything You Always Wanted to Know About Sex (But Were Afraid to Ask) (1972), Burt Reynolds plays the master controller of an unseen man's body, while Woody plays a sperm.
Parodied in Men in Black, where the giant guy (played by the guy who played Lurch in The Addams Family movies) really is controlled by a tiny alien.
- Lurch guy (played by Carel Struycken) was the one whose body temperature rose after death and the gentle jeweler (played by Mike Nussbaum) was the one with the tiny alien in his head.
- They were both androids controlled by the tiny aliens.
A big part of the premise behind eXistenZ.
The three spirits in the 2009 CGI film of A Christmas Carol are depicted this way, and all are played by Jim Carrey, the same actor as Scrooge.

Literature

This comes up from time to time in the Discworld series, especially with the character of Sam Vimes. He has a number of ghosts, including the Beast, who is the part of his brain that wants to inflict his own view of justice on the world, and the Watchman, who doesn't let him.
- This is especially popular among the witches. Agnes Nitt, a witch "with a wonderful personality," who hates that role, has a sassier alter ego named Perdita X. Dream, and Perdita's interference prevents her from the dreamy vampire's Mind Control. It turns out Agnes isn't alone, as the Reverend Mightily Oates has a Good Oates and a Bad Oates, who disagree on theology and life philosophy.
- Granny Weatherwax is implied to have this. She's a natural Bad Witch, but since her sister ran off to be evil she has to be good, and her evil impulses are kept firmly in check by her own iron will, even if throwing off her constraints would let her pretty much deal with every threat that comes her way in minutes.

Live Action TV

One could argue that Baltar's hallucinatory Six on Battlestar Galactica fills this role; she spends an awful lot of time doing his thinking for him, especially as he tends to be rather useless in a crisis. Of course, there's always the possibility that she's something else entirely...
- The same could be said of Six's ghost Baltar, for that matter.
- Or Baltar's ghost Baltar! ...You know what? We give up trying to figure this one out until Ron Moore explains it.
  - The finale suggests that they're angels, or maybe demons
Shows up in Dollhouse. Namely, the "other personality" type.
In the Stargate SG-1 episode "Grace", a little girl appears to a concussed Carter and helps her find the solution to her problem. The rest of her team and her father also appear to her at various times, representing different aspects of her personality (eg: Teal'c as the seasoned soldier).
- In the mirror episode "Grace Under Pressure" from Stargate Atlantis, Carter appears to McKay as the genius-part of his mind trying to stop him from killing himself.
An episode of Corner Gas had this, in Hank's head. Lacey almost shows him how to open a notoriously difficult carafe, but he stops her, saying he has a limited amount of room in his head. Cut to two a Hank sitting at a desk in front of some boxes. Another one comes up to him to place a box of Bananarama lyrics. A minute later, Hank tries to tell a joke, but he says "Bananarama" instead of the proper punchline. Cut to his head again, where the boxes have all fallen and mixed together.
Depending on your interpretation, this could at least partially be what drives the odd behavior of Cameron from The Sarah Connor Chronicles. The episode "Allison from Palmdale" implies that the "Allison" persona she adopted could be influencing her actions in many ways, especially considering that she becomes Allison at one point.
In the The Mighty Boosh episode "Journey to the Center of the Punk," the ultimate destination of Howard's Fantastic Voyage is Vince's brain: a lone cell who looks like Vince and spends all its time watching a television that only shows people who look like Vince.
In Seinfeld, Jerry is dating a girl who is gorgeous and sexy, but not very bright. His conflict over this manifests itself in a scene where his brain (Jerry in a brain-shaped hat) and his penis (Jerry in a military helmet) face each other off in a chess game until one folds.
Lizzie McGuire^[context?]
In Farscape, over the course of the series, John has had everything from retreating into his inner self to try to work ideas out, to literal multi-layered wars inside his mind. On a day to day basis, his inner self usually has prolonged conversations with Harvey, Scorpius's mind clone who is mostly almost not entirely trying to help John. ...Maybe.

Music

Ayreon built a whole two-disc album around this. In The Human Equation, the main character—named "Me"—goes through a metal opera interacting with different aspects of his personality: Pride, Reason, etc.
"Driver" by Phish:

Let me tell you about the driver
Who lives inside my head
He starts me up and stops me,
and puts me into bed...

Newspaper Comics

Several times in Calvin and Hobbes, Calvin has had little mini-Calvins operating his body and screening his dreams as films.

Religion

This is a central doctrine in any religion that believes in an immortal (or killable, for that matter) personal soul, including Christianity, Islam, Hinduism, and some branches of Buddhism: You do not have a soul, you are a soul; you have a body; the soul is the driver, the body is the car.
- But note that this is a comparatively recent religious interpretation. The bulk of Christian theology, at least up through Thomas Aquinas, makes it very clear that a you are a body and a soul, and a disembodied soul is inherently incomplete. In the very early church, going around claiming that "you are a soul; you have a body," would be considered dangerously close to gnostic heresy.
  - Actually it's backwards. The original interpretation going back to Judaism was that you are a soul, and that soul consisted of the mind, body, and spirit. To use the analogy above, the mind is the driver, the body the car, and the spirit the car battery; the soul was everything together.
  - And sometimes the distinction was so blurred, people thought that the soul was an actual organ within the physical body.
    - Said organ is commonly referred to these days as the brain.

Video Games

The Sims and its sequels are a computer game expression of this trope, in that the player serves to control the Sims' every move.
The final villain in Sam & Max: The Devil's Playhouse is revealed to be one of these - specifically, Max's super-ego, plotting to destroy both of them and a huge part of New York in order to save both others and himself from having to put up with Max.

Web Comics

Comedity. What video gamer doesn't have a Personality 47, aka "The Red Right Hand"?
King of the Unknown co-stars Leonardo da Vinci, who on his death bed built one final, great invention to contain his spirit, so that he could continue to roam our plane of existence. In his now-robotic body, the modern-day "Vinny" acts as an agent of the U.S. Government Agency of Fiction known (to few) as IRSU. There, he constructs various technological wonders necessary to investigate and eliminate forces of the unknown and supernatural. He is also the roommate and best Robot Buddy of the series' titular protagonist, the King of Rock'n'Roll.
In Narbonic, all the characters have swarms of pixies that sometimes appear around their heads and represent aspects of their personality. They have iconic outfits that show what they represent. Most characters have an angel and a devil, but sometimes the angels are evil too. Interestingly, while the characters can only see their own pixies (and only when the pixies are talking) pixies can see the pixies of other characters and communicate with them when both sets are active.
Order of the Stick had an arc where Haley lost the ability to speak properly and had inner-monologue conversations with various facets of her personality, including her self loathing, her optimism, her vanity and her latent bisexuality. Only one facet was present in the beginning, but more started showing up, and they even lampshaded the fact that Haley was probably going crazy.
Ménage à 3: Most of the cast seems to get Shoulder Angels, but Sandra has her id, ego and superego debating whether or not Didi is flirting with her.

Western Animation

Family Guy does several gags based on this. In one instance, two accountants are seen working inside Peter's skull as he suffers a hangover. In another, we cut to the inside of his brain, as the last brain cell (in homage to a Twilight Zone episode) reflects on having time enough at last to read all his books...only to suffer the same terrible fate as his Twilight Zone counterpart.
- And in yet another episode, someone uses the word "esoteric" while speaking with Peter, and it shows a board of directors inside Peter's head trying to figure out the definition of esoteric. They decide it means "delicious", and Peter continues the conversation as if this usage of the word is perfectly normal.
The Simpsons has Homer converse with his brain several times. They generally have an antagonistic relationship. ("Shut up, brain, or I'll stab you with a Q-Tip.")
- This happens to other members of the cast, as well; for example, when Lisa becomes a popular kid because of her pool, her brain tries to advise her it's fleeting. ("Shut up, brain! I have friends now! I don't need you!")
- Homer is so stupid that his inner self is usually shown as being something similar to of those toy monkeys banging the cymbals. Subverted in the movie, when the toy monkey in his mind is going off while Marge is talking, and it drops the cymbals and forces Homer to listen to her.
- Homer's brain has actually given up and left him to go it alone on at least one occasion. It is, however, kind enough to remind him that money can be exchanged for goods and services.
- Seen once with Marge, and implied that she actually has several inner voices, each one residing higher up in her beehive. The one on top simply says "Why are you asking me, I'm just hair; your head stopped eighteen inches ago."
A number of shows have applied the trappings of Robo Cam to human characters, including The Simpsons and Coupling.
SpongeBob SquarePants used a clever subversion:

Tiny Spongebob #1: Hurry up! What do you think I'm paying you for?
Tiny Spongebob #2: You don't pay me. We don't even exist. We're just a clever visual metaphor used to personify the abstract concept of thought.
Tiny Spongebob #1: One more crack like that and you're out of here!
Tiny Spongebob #2: Please, no! I have three kids!

Darkwing Duck explained that everyone has a "little hero" trapped inside their mind. Actual heroes have them free and in charge. Villains have them tied up and gagged. Darkwing's is not only free, but partnered with a grotesque monster that represents his ego.
Reason and Emotion, a Disney Wartime Cartoon, revolved around this concept. Apparently, the inside of one's head is like a car, and inside it are Reason (a prim and proper guy in a business suit) and Emotion (an unruly caveman). When Reason is in the driver's seat, everything is fine, but when Emotion is in charge... well, apparently you run the risk of turning into a Nazi. The short ends with both Reason and Emotion as pilot and co-pilot on an Allied bombing mission.
In an episode of The Fairly OddParents, Timmy travels inside Vicky's brain to find that it is run by an army of computer technicians. It's revealed that Vicky is so nasty because the technician responsible for controlling her "nice" emotions never showed up for work.
- Another episode involves Timmy wishing to have no emotions, which resulted in the emotions flowing out of his head in the form of colorful little characters(such as a white square for Common Sense, a pink heart for Love, and a green thing for Envy).
A very literal example in Transformers Generation 1 Season 3, the episode Ghost In The Machine, deals with the ghost of Starscream, who is literally able to possess machines (other Transformers).
In one episode of Two Stupid Dogs, Little Dog is trying to think of a plan, and we cut to the inside of his head, where his brain has an "OUT OF ORDER" sign hanging from it, and a sad little repairman sitting next to it and lamenting "I can't fix it! I just can't fix it!"
In the Teen Titans episode "Nevermore", Beast Boy and Cyborg find themselves trapped in Another Dimension which is really Raven's mind, inhabited by copies of Raven with different personalities and costume colors—as well as her demonic father and some creepy red-eyed crows.
In Brandy and Mr. Whiskers, Whiskers' brain is a separate entity in the vein of this, and for some reason he's Jewish. On multiple occasions, he gets fed up with Whiskers not paying any attention to him, and leaves. This doesn't seem to slow Whiskers down, although he's invariably despondent that his brain has abandoned him.
Once Upon A Time... Life used this metaphor extensively, up to the point that the nucleii of every cell in the body were represented by fully staffed command centers.
An episode of Jimmy Two-Shoes had two racing bugs climbing into the brains of Jimmy and Beezy and finding little one-eyed blobs in the driver's seat. Jimmy's happily gives up his post when requested, while Beezy's is asleep on duty.

Other

Some people who experience the phenomena referred to as multiple personalities (or MPD or DID, if you're a doctor) report having spaces within their minds where the various selves interact and converse.
At one time Epcot had an attraction called "Cranium Command" which was built around this trope. The hero had to "pilot" a twelve-year-old boy through his day with the aid/hindrance of the body's various organs, glands, etc. Especially noteworthy for Bobcat Goldthwaite's tender, nuanced performance as the adrenal glands. Curiously, the people who controlled the world's brains seemed to be randomly assigned and fired from hosts at random, one day piloting a chicken and then one day piloting a 12-year old boy.
Internet comedy group Britanick have done a sketch about this.
Swedish comedy group Galenskaparna had a routine in which a man's brain gets so tired of the man never using it, that it escapes and tries to make a new life for itself. ("Does anyone want a brain? Practically unused, only one previous owner!")
A commercial for the Sega Saturn featured the effects of playing said system. These effects were shown via a Ghost in the Machine. Not only the brain, but the eyes, ears, nervous system, etc. This commercial has been placed as indirect Nightmare Fuel due to the ending, which displayed the person's bowels literally malfunctioning from playing the Sega Saturn too much.