"PAIs tend to be able to present more natural user interfaces than the expert systems they compete with, tending to be at least vaguely self-aware, and much more responsive to and on emotional levels. In particular, niche market and custom built models are limited only by legislation requiring that entities surpassing a specified set of standardized metrics cannot be considered property, and must be registered as either customchildren or custom dependent employees. While the difference is clear for low end models, standards aside, most will agree that the line between a high end PAI and a designer cyborg human is exceptionally blurry."
Wetware refers to a biological system and typically refers to the human brain and nervous system. It can also come to mean bacterial computers and organic based processing agents.
In speculative fiction settings, particularly those where true artificial intelligence either does not exist or is shunned, it is sometimes the case that the brains of living beings, sapient or not, will be incorporated into machines and used for processing or command and control purposes. It varies whether the rest of bodies are retained.
Related to Brain in a Jar and Man in the Machine. Compare Brain Uploading, Brain/Computer Interface, and Living Battery. See also Human Resources.
Contrast Wetware Body, Tinman Typist.
In episode 2, "Proof of Recklessness: TESTATION", a dead man's cyberbrain was wired into a HAW 206 Tachikoma-style tank. The tank goes berserk, and Section 9 must stop it.
The CEO of an organ-cloning facility ended up choosing to keep his brain stored in a miniature, boxy robot rather than moving to a humanoid chassis.
In a subversion, an AI-controlled Tachikoma faked having a real brain inside his chassis to distract police from the child they were questioning.
To some degree, full-body replacement cyborgs meet this. The only thing that remains of their body is a brain inside a human-shaped chassis. As mentioned by Batou at one point, the bodies they use are largely impersonal objects. He advised the female Major that she should upgrade to a male chassis for improved strength.
The Zentradi Mobile Fortresses of Macross are each commanded by an ancient Supreme Commander who is integrally fused to the ship.
In Outlaw Star Melfina serves as the navigation system of the titular ship. Fortunately she has considerably more freedom than most wetware CPU's and can disconnect from the ship when it isn't in flight.
In Gundam Unicorn, some characters theorise that the NT-D uses a combination of the psychoframe and the pilot as a living (and highly efficient) battlefield processor. It works extremely well, but appears to verge a little too close to Ax-Crazy at times.
In Sonic the Comic, Dr. Robotnik's plot during the buildup to issue #100 involved connecting Sonic the Hedgehog's allies the Emerald Hill Folk to a machine to form a gigantic wetware CPU.
Film example that did not come to pass: The original proposal for The Matrix had the machines keep humans in the matrix in order for their brains to act as a great neural network. (Without taking the brains out of their bodies, note: the rest of the film would have been the same as what we got.) This of course makes far more sense than the physics-defying "power generation" explanation given in the completed film, but it was apparently changed because the studio thought the original reason would be too hard to understand.
This explanation for the Matrix survives (in the form of a passing mention) in the Neil Gaiman short story "Goliath," written to promote the movie.
Some fans just still pretend that this is in fact the case and that the humans only got a simplified understanding of the situation due to their limited access to information about the machines. In other words, the reverse of Fanon Discontinuity.
RoboCop was made specifically to compete with the ED-209 in RoboCop (1987), which was fully robotic. The human element of Robocop would allow him to have better judgment. It is successful because the ED-209's AI proves to be... faulty.
In The Ship Who Sang, handicapped children are placed in titanium life-support capsules and trained as human computers for starships.
The Wild Cards novel Double Solitaire has Dr. Tachyon's Axe Crazy grandson (in a stolen body) turned over to the Network to become the lobotomized organic processor for a mining machine, in order to to pay off the debts of the guy whose body he swiped.
Some of the Berserker stories of Fred Saberhagen had the killing machines attempt to use organic brains to introduce more fuzzy logic into their tactical computers.
In the Nightside series, the Collector is served by a small army of robots built with Catgirl features and directed by living cat brains.
Conjoiner drives in the Revelation Space universe by Alastair Reynolds always contain a Conjoiner brain, who controls the reaction. Another Conjoiner who almost became one likens the experience to spending your life playing a challenging video game. However, the Conjoiners keep it quiet because they expect other humans to react badly.
M. John Harrison's Light features K-ships, each one a heavily armed starship built around alien technology interfaced with a cybernetically altered human in an amniotic vat. The process of conversion is permanent and more than a little nightmarish, and most of its recipients are children or young teenagers.
The space-faring slavers from Vernor Vinge's Tatja Grimm's World'' kidnap people, remove their brains and then fit them to a computer that suppresses their personality without totally trashing their intellect, to form a useful Wetware CPU.
The head of Gerald Metaclura is the main computer of the Generation Ship in Mayflies by Kevin O'Donnell.
From Otherland, the Other is the brain of a telepathic human infant jacked into a computer and used as its operating system. Further, additional unborn fetal brains were harvested and stuffed in there with it to give it additional "capacity". It's half-insane from the cruelty and deprivation of its existence, and seeks a way to turn against its masters.
This is also the reason that spice is so incredibly valuable. The Corrino empire could probably survive without its Spice addicted nobles, but the substance is vital to the transformation of normal human beings into Navigators and their maintenance. It becomes less so during the Scattering, when machines are developed that replace Navigators.
In Frank Herbert's Destination:Void, the Voidships are also guided by an OMC - Organic Mental Core (Herbert did despise euphemisms for crimes against humanity, but he could churn them out with the best of them).
Larry Niven's Known Space short story "Becalmed in Hell" has the brain jar of Eric Donovan, who was mortally wounded in an accident, installed in a spaceship designed to explore Venus.
In William Shatner's Quest For Tomorrow books, Jim Endicott's biological mother develops a way to link human minds to create the most powerful computer in the galaxy. Her partner (and lover) only known as Delta usurps the technology and uses it to gain power for himself and influence for Earth (by offering to solve any problem the aliens have). Unfortunately, the process of running calculations is not perfect. Every time it is used, thousands of people inexplicably go insane, raping and killing anything around them. Publically, this "madness" is blamed on drugs. However, it turns out that Jim's mother later perfected the process and encoded the information in Jim's DNA (or did she?). This new process has no unpleasant side-effects but requires that the subjects be consciously aware of it and be willing.
Just to illustrate how powerful this "computer" is, the novels have a small fleet of human warships defeat an armada of much more advanced alien ships by taking complete control of the ships and using near-perfect tactics.
In the 'Biofab War' space opera series by Stephen Ames Berry, written back in the 80s, one of the most feared fates that can befall a person is to be 'brainstripped', to have their brain forcibly used as a CPU for the control system of enormous space battleships called 'mindslavers'.
In There and Back Again by Pat Murphy, this is the Resurrectionists' hat. They only do it to clones (and unintelligent animals) for ethical reasons; that doesn't much help the protagonists, however, as nearly all of them are clones of each other...
In the universe of the Hyperion Cantos, this is one of several ways to attain AI, through the creation of artificial brains and DNA-based computers (other AIs had created the TechnoCore). Many of these control spacecraft, including The Consul's yacht (that particular AI also has a sense of humor, providing much comic relief). It is also revealed that the TechnoCore uses the processing power of every single person plugged into the Internet for their calculations. And then it gets worse...
A large number of Philip K. Dick novella use this trope. Often to Mind Screw extremes. And often inverted to further the Mind Screw and gaslight his readers into a state of dissociative fugue. Have fun doubting your sanity.
In Asimov's short story The Monkey's Finger, a capuchin monkey has his brain surgically altered to turn it into a computer capable of generating stories and books of the highest literary quality. The story deals far less with the bioethical and technological implications than how it will affect writers.
"The Girl in the Fireplace" had this as the Monsters of the Week's aim with the titular girl.
In "Bad Wolf", the Daleks use one to control the operations of Satellite Five, installing her at five years old.
There's another Dalek-aligned one in the classic series serial "Remembrance of the Daleks".
The Daleks themselves are basically squid-like aliens from the planet Skaro who are permanently encased in a virtually indestructible R2-unit.
In the classic series, it's implied the Logopolitans interface much more intimately and directly with their computers. They also have gigantic brains protruding from the back of their heads.
Parodied in the Doctor Who New Adventures novel SLEEPY, where the Mad Scientist who has built a telepathic AI insists that neural nets are completely unnecessary. Apparently one of his rivals tried to create an intelligent computer by hooking a cat's brain to a mainframe, and got "a computer that wants to play with string and sit on your newspaper".
The people on Satellite Five in "The Long Game" have ports in their heads to input information and process it. Adam, a temporary companion, gets one himself, which is why The Doctor throws him out of the TARDIS. The Controller worked on the same principle, only that was her entire life.
"The Talons of Weng Chiang" gives us the Peking Homunculus, which is powered by the brain of a pig. A particularly vicious pig.
Enterprise had a space station that stole brains to keep itself running.
Star Trek: Voyager has neural gel-packs to assist in certain computer functions that require that organic touch.
In Andromeda the Consensus of Parts used human neural matter to satisfy the requirement for organic intuition to navigate the Slipstream.
In Babylon 5, the Shadow starships all used captured lesser races members as pilots fused with the hull.
Lexx's 790-model cyborgs consist of robotic heads attached to the decapitated bodies of executed convicts. A small cube of human brain tissue is used to give the drone its higher functions, such as the capacity for a (rudimentary) personality.
In Dollhouse people sent to "the Attic" have their brains networked to make Rossum's supercomputer.
The Cyberax arc of Bugs was basically The Matrix, only without the need for it as the wetware is clinically dead.
In the new Battlestar Galactica, the Cylons' ships — or at least their FTL drives — are controlled by "hybrids," human-looking women who lie in a tub full of goo hooked up to cables that look a lot like the ones in The Matrix; Razor establishes that they were created by experiments involving vivisected humans. The hybrid constantly babbles a stream of partly-technical, partly-prophetic-sounding, partly-nonsense words, but doesn't seem conscious in any real sense most of the time. When the Cylons give the order to make an FTL jump, the hybrid gasps "Jump" orgasmically as the ship does so. When such an order is about to be given at a very significant moment:
Hybrid (crying out in apparent pain): Mists of dreams drip along the nascent echo and love no more. End of line.
Number Five: The Hybrid objects.
Number Three: She doesn't get a vote. Jump the ship.
The Borg Queen in Star Trek is one of these; not merely an ambassador like Locutus but a being that functions as the hub of the collective consciousness.
Walter can step inside Automan and temporarily fuse with him.
Pilot from Farscape is symbiotically joined to Moya a leviathan. While Pilot controls the crew's life support systems and pilots the ship, Moya is capable of moving on her own and can disregard Pilot's instructions if she has to.
Moloch, from Buffy the Vampire Slayer, who was a demon whose essence was put first into the Internet and then into a robot body.
In Total Recall 2070, Alpha-class androids (still on the prototype stage) use cultivated neurons. Alpha technology is not yet fully understood, as android inspector Farve experienced weird "connections" with people under an Alpha Mind Control implant.
In the Red Dwarf episode DNA Kryten states that his brain includes a bit of biological material, which is apparently enough for the DNA conversion machine to make him fully human.
Used extensively in Warhammer 40,000, in which non-sentient servitors (robots with human brains for CPU) are very common. Also, some ship captains are permanently wired into their vessels, and in the novel Storm of Iron, there is a tech-priest who has discarded everything but his brain and wired himself into the main computer in the facility he commands. The Space Marine Dreadnoughts, fighting machines piloted by mortally wounded super soldiers permanently encased in a life support sarcophagus might also count.
Indeed, this is compulsory for the Imperium - any significant levels of AI are explicitly forbidden, due to a Robot War sometime in the 20 or 30,000s. Anything over a very low level of intelligence has either a human operator, or a human brain. The Imperium being the Imperium, of course there are exceptions: The Land Raider tanks used by the Space Marines are suspiciously bright for an entirely artificial machine. In some cases, they've fought battles by themselves after their crew was knocked out or killed. But since they're ancient and venerable machines, that's alright - when the borderline-holy Adeptus Astartes do it, that means it's not illegal.
In the Horus Heresy novel The First Heretic, a marine explains to a civilian why they're attacking a planet that has robots: According to him, "mineral" intelligences always have thought patterns incompatible with organic ones, which inevitably leads to rebellion.
In miniatures game Legions of Steel, the eponymous Machine Empire captures humans and other sentient beings, keeps them in a dream state while holding them in a pod (similar to the Matrix, but 5 years before the movie). Machines, having no truely creative or lateral thinking abilities, use chemical torture on their captives, read their thoughts - nighmares - and search through them for new ideas. While the Machines searched for ideas with technological application, the side effect was to incorporate horrific images into the design of new fighting robots.
Later, the Machines experimented with wetware and artificial brains with true sentience. Unfortunately for the Machines, with true sentience comes free will, and some of the sentient machines (Omega Class) rebelled against the Machine Empire to side with the organic civilizations.
The Gamma World had Think Tanks, which were human brains connected to computer systems.
In Deadlands: Hell on Earth, automata are machines with zombie brains (controlled by a demon) wired in as the CPU. Cyborgs are Harrowed (ensouled undead), some of whom go so far as the Brain in a Jar route.
The Mi-Go in Cthulhu Tech use human brains like this. The consciousnesses inside them still function however, and are allowed to form social networks so as to remain sane and productive. You just know this'll come back to bite those aliens in their collectively non-existent ass someday.
In the Underground RPG, there are "bio-drives", which are basically human brains (donated willingly or otherwise) which act as huge-capacity storage media. There are rules allowing Player Characters to sell their existing brain off as a bio-drive and have an artificial brain implanted.
The various biomechanical races of the Matoran world in BIONICLE all have some organic parts, but we don't know if the brain is one of them. The Bohrok, though, play this dead straight, being robotic drones "driven" by organic Krana parasites.
Starcraft has the Protoss Dragoons and Immortals - the broken bodies and brains of half-dead soldiers, wired into walking tanks so that they can continue to fight.
These are directly inspired by the previously mentioned Space Marine Dreadnoughts.
The Adjutant was one originally. Female human, head connected to various wires and bits of machinery, presumably to aid in briefing the player in missions. It has been retconned to be entirely robotic, probably to make the "good guys" less squicky.
In Homeworld, the mothership would have needed an unworkably large bridge crew to handle all command and control tasks, and they could not make an AI to deal with them for certain reasons. Neuroscientist Karen S'jet came up with a plan to use a brain for the task and insisted that she herself be fitted into the ship.
She reprises her role in Homeworld 2 in the new mothership, the Pride of Hiigara, a century later.
In Half-Life 2, the Striders actually have organic brains, which the player gets to see when Dog rips one out in a scene in Episode 2. Probably the same goes for other Synths used by the Combine.
This is very likely, since the other synths used by the combine are other races that have fallen to the Combine.
EYE Divine Cybermancy allows the player to replace their nervous system with a top-of-the-line computer system, interfacing with the brain for much more improved reflexes. At least, according to vanilla text - the real in-game effect is heightened agility.
In Vega Strike 'verse "Pseudo-AI" is used for most tasks where a "true" AI would be too expensive and a simple computer isn't creative enough. "PAI Wetware" is one of legal goods, a thousand times or so cheaper than AI cores. The Rlaan as proponents of Organic Technology carry it further and creep out the humans by equipping armed drones with pet brains.
The Strogg from Quake II couple their computers with organic beings, including a factory that mashes humans into Stroyent that has a creature's digestive system working as part of it and a gigantic brain with cybernetic implants in it as their main communication system processor. They're also fond of "Stroggifying" enemies in a method more brutal than the Borg, implanting cybernetics via surgery without any anesthetic whatsoever.
CABAL the evil supercomputer from Command & Conquer apparently is the "Computer Assisted Biologically Augmented Lifeform"; it draws some processing power from human beings. At the end of Firestorm CABAL is apparently keeping Kane alive.
More specifically, the Biological Augmentation appears to consist of a roomful of Kane clones all hooked together. At the line "Our directives must be reassessed," the individual Kane appears to have merged with CABAL.
At the end of Deus Ex, you are given the choice of merging your character's consciousness with an AI called Helios. The sequel shows that this was the canon choice.
One ending of the sequel involves this happening to Everyone.
In Deus Ex: Human Revolution, the fact that Panchaea required this of three women (who are obviously still conscious of their fate when you find them) was one of the factors involved in Hugh Darrow's Sanity Slippage.
And in "The Missing Link" DLC you witness the horrific process involved in creating them.
The Biodrones from X-Com: Terror from the Deep look an awful lot like brains mounted in flying saucers. They are. Human brains, literally butchered into obedience, and fitted with a sonic weapon where their voice box used to be so they can scream their targets to death.
In the various Fallout games there are "Robobrains", basically a brain in a jar connected to a robot body. From their voices in Fallout 3, it seems only women's brains are used.
Some of the in-game characters claim that monkey/ape brains were supposedly used (unlikely considering the brain is too small for that). Others, that criminals were utilized as human resources. One way or the other, chances are the brain has only been reprogrammed to sound like a woman, so yeah...
Apparently, the designers of the Vaults figured that a pornstar's brain is a good choice to run a computer.
Mr. House in Fallout: New Vegas essentially turned himself into this, to make himself effectively immortal.
And then there are the Think Tanks of Old World Blues, robots powered by the brains of Mad Scientists so that said scientists can do experiments After the End.
They also do this to the Courier against their will, although the Courier somehow manages to remain fully self-aware without their brain, much to the Think Tanks surprise. Eventually leanding to the bizarre situation where the Courier has a conversation with their own Brain in a Jar and can even hit on it.
Courier's Brain: Are you... Are you coming on to me?! Sweet Lord, I don't even have the words for how repugnantly wrong that is!
Joker expresses this fear regarding giving control of the Normandy to EDI in Mass Effect 2:
"See, this is where it starts, and when we're all just organic batteries, guess who they'll blame? 'This is all Joker's fault! What a tool he was! I have to spend all day computing pi because he plugged in the overlord!'"
In Borderlands 2, it's revealed that The Guardian Angel that serves as an Exposition Fairy in the game is not a sentient A.I. as she claims, but a Siren named Angel hooked up to machines and constantly pumped with Eridium by her father Handsome Jack as a tool for his schemes.
The End of Flesh expansion to Sword of the Stars 2 adds these. The lore explanation is that they are meant to emulate the abilities of the Loa without actually using AI.
The fanmade mod "Marathon: Rubicon" features an AI named Haller at the beginning, who is known to be a wetware AI. Tycho explains later that Durandal destroyed him out of jealousy.
The Journeyman Project's first two games utilize electronic "Bio Chips" which can be collected to employ certain functions.
How they actually work is explained in Buried in Time, and is also what the AI Arthur is. Both are made of "Neuro-synaptic polymer gel", essentially synthetic brain networks that allow any computer to get better at its tasks.
In Ilivais X, the Phonos Weapons (which include the titular mech) are supposed to use their pilots like this. While they CAN be used with motion control, they tend to be controlled via mind synchronization. The four pilots are altered to be fragile, intelligent, and highly emotionally derailed, because the intent is that they stay in their unit until they are destroyed (which, given their effective regeneration and the pilots' immortality, may well never happen), turning into sentient processors for their machines.
Common in Orion's Arm, though the prevailing idea is that wetware can only get you past the second singularity or so. The lums of the Red Star 'M'Pire went and disproved that by creating the Silk God, a completely organic archailect possibly of the fourth toposophic. However, being the size of a solar system, it's still a lot less efficient than diamondoid-based inorganic fourth-toposophic 'J-nodes', which are only as big as large gas giants.
In Star Army (A sci-fi roleplaying site) due to their more primitive technology, the race known as "Gartagens" use these as the AI networks of their spaceships. Since they're depicted as OCD compared to humans, this actually does put them on an almost equal AI footing with the other races of the setting. 
Narbonic had an arc called "Professor Madblood and the Wetware Interface'', in which Madblood used Dave's brain to power a giant robot.
Carbon computers in Among The Chosen are carried by female, transhuman hosts by means of artificial pregnancy. It is not clear whether the computers have a personality of their own or is an extenuation of their host.
Skinhorse has Nick, a perverse foul-mouthed helicopter who was once a gamer and web troll until he had his brain scooped out, rewired, and shoved in a jar. Nick may well be the first cyborg brony if In-Universehints are correct. Particularly interesting in that part of the plot is him coming to terms with this to such a point that he now self-identifies as a machine and has joined a robot union.
In Sequential ArtQuinten R&D has four "organic processors". Unusual in that they aren't Brain in a Jar type, but squirrel girls with radio-implants linking them into Hive Mind called "Think Tank". Also, this provides some sort of Cyberspace interface with true computer AI. They still have free will, if somewhat brainwashed.
In Axe Cop, Wolver Man's cyborg pet Iron Spider Cannon is driven by a mouse brain wired into its circuits.
The ψiioniic, Sollux's ancestor in Homestuck, ended up becoming something like this. Thanks to his powerful telekinetic abilities, he was enslaved by Her Imperious Condescension and harnessed as the living battery for her flagship. It's unclear how much consciousness or control he has left in this state, but since the rest of the ship appears inorganic this trope still applies.
Currently, in Sonic the Comic Online, Robotnik has become part of a Drakon super-computer and has launched a massive invasion of Mobius in a bid to become the planet's proxy ruler under control of the Drakons.
This includes Richard Nixon's head borrowing Bender's body to get elected, and in the first 'movie,' Hermes (who had been decapitated) controls the entire Earth fleet, using his Super Bureaucracy Skills, for a Theme Song-Boosted CMOA.
The Jonny Quest The Real Adventures episode "DNA Doomsday" involved an organic supercomputer that was built from the DNA up to be a perfect data processing system. When a simulation is run to test the system, a serious error caused the organism to go on a rampage and try to test the simulation in real life. The simulation? Is it possible to destroy the military base that the computer was being built in.
In Phantom 2040, Maxwell Madison was murdered only to have his memories downloaded into a computer, which his wife uses/abuses to resurrect him in the body of several successive biots. Most attempt to commit "suicide" than stay with the psychotic woman, however.
In the Spongebob Squarepants episode "Welcome to the Chum Bucket", when SpongeBob refuses to work for Plankton after Krabs lost his contract in a poker game, Plankton puts his brain in a robot chef. Funny how he didn't consider that a robot with SpongeBob's brain would be just as stubborn as SpongeBob.
In the Teenage Mutant Ninja Turtles 2003, after being severely injured for his failures, Baxter Stockman goes through a series of mechanical bodies, losing more and more of his real body at each step.
Also played with during the first Fast Forward season of the series, the turtles find the journal that Cody Jones had used to learn about them. Once the temptation to read it becomes too great, they read a series of entries centered around each of the turtles. Donatello's entry (much to his horror) states that, after an accident in deep space, his brain is placed into a robot known as the Serling unit. Fortunately for the turtles, it turned out the journal they were reading was a fake prepared by Splinter and Cody when they knew the turtles couldn't resist reading it.
Megamind's brain-bots are implied to be this, though the closest thing to a brain one can see is a plasma ball.
Hybrots are robots with partially organic CPUs made by spreading rat neurons suspended in a nutrient solution on a computer chip. They've only lived a few weeks to a couple months so far, though with better life-support they could live up to two years.