Some space ships aren't just big pieces of metal that happen to fly through the stars. Some can think intelligently, and even interact with the other characters. Sometimes the ship is a true example of Mechanical Lifeforms. Sometimes this occurs because of an advanced AI in the case of a mechanical ship. Sometimes the ship is actually a living being. Occasionally the ship is a hybrid of the two with a living being grafted on to a ship to the point where they become one entity. Whether the ship is actually alive or not is generally a matter for the work in question to resolve.
Generally when these are seen in fiction they're female thanks to a long maritime tradition. Often represented by a Spaceship Girl, the ship's walking talking female avatar.
This trope does not cover ships that are organic, but do not think on a level higher than simple animal instincts. Those are covered by Living Ship. It also does not cover ships that happen to have AIs when those AIs are treated as separate entities that are not integrated into the ship itself.
Acting as both a character and setting, the sapient ship is perhaps the best example of the Fisher King, as the environment quite justifiably mimics the ship's mood, health, and situation.
Of course, looked at rationally, it's not clear that it is desirable for a ship to be sapient, at least from the point of view of the crew. If the ship is happy things tend to run smoothly, but upset a sapient ship and you might wind up locked in your quarters or having your life support cut off.
Despite the problems that can arise from the setting having a mind of its own, there are narrative advantages. Having the ship able to take over roles such as pilot, and navigator cuts down on crew requirements (and thus cast size) which in turn cuts down on life support and accommodation requirements, sometimes to the point where a crew may be an optional extra. The level of sentience and independence will determine just how much of an advantage this is.
Not to be confused with Setting as a Character where the ship is just treated like a character by the cast but isn't necessarily alive. Compare Sapient Steed which is this trope applied to steeds and smaller vehicles that are used for transport instead of living on. Some Sapient Ships are big enough to be Genius Loci. Spaceship Girl is a subtrope when the AI creates a humanoid avatar that is an attractive woman. When this is accomplished by plugging a human brain into the computer, it's Wetware CPU.
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Anime and Manga
Tenchi Muyo!: the Juraian spacecraft are powered by living, semi-sapient trees. The parent of them all is not only fully sapient, but a goddess - and the alter ego of a main character. Also, Ryo-Ohki, who is the cute mascot character that transforms into a Living Ship.
Infinite Ryvius: The Vaia Ships are mostly technological, but each has a living Vaia at its core. The Vaia are sapient, though only one is a full-fledged Spaceship Girl.
Outlaw Star: the titular ship has a sapient onboard AI, but must also be connected to the Spaceship Girl Melfina. Near the end of the series, Hazanko's mind and body fuse with his spaceship, forming partially-biological version of this trope.
Captain Harlock series portrays the Arcadia as a living ship, after Tochiro uploaded his mind in the computer, or, depending on the series, died and started to haunt the ship. Various incarnations reveal the Arcadia to be able to empathize with the crew, hold nonverbal conversations with the Captain, and even move around without a physical pilot. This is also an unusual example of a sapient ship being explicitly male.
One Piece: The Going Merry proved to be just this as early as the Skypeia Arc, when Usopp saw a spirit repairing the Merry. Many arcs later, Franky revealed that Usopp saw a manifestation of the soul of the Merry, which developed because the ship was loved and cared for deeply. Later on in the same arc, the Merry's status as sapient is driven home when the ship itself comes back to save the Straw Hats at Eines Lobby. Later on, the Merry finally collapses due to all the damage it's took thus far in the series and the Straw Hats give it a Viking Funeral. Luffy laments that they never took care of the ship properly, but the Merry speaks to them, stating that it held no ill will and that it was happy to be with them.
The Authority: The Carrier - a spaceship that, while being made of metal, is fully sapient. However, it has only once spoken directly to anyone (and then it was only to tell hapless assassin Kev Hawkins what a prick he is).
X-Men: The Brood used lobotomizedSpace Whales for transport, and the surviving ones at liberty were both sapient and not happy at all about the situation.
The original X-Factor team liberated a Sapient Ship that was enslaved by Apocalypse, named, appropriately enough, Ship, which had a long and varied career in the various X-Titles over the years. It happily became friends with X-Factor after they freed it from Apocalypse, and served as their base of operations, home, and long-range transportation. Ship was a several thousand year old piece of Celestial technology and the size of a large skyscraper, being so huge that, while in it's usual docked location of standing on-end in a building lot, it became a well-known part of the New York City skyline. The physical form of Ship was later destroyed in a final battle with Apocalypse, but the artificial intelligence survived by downloading itself into a small module. It soon traveled into the future with Cyclops's son Nathan, who later became Cable, and the intelligence of Ship eventually became Cable's space station Greymalkin, and then eventually his floating island Providence. At one point a copy of the AI was even downloaded into Cable's techno-organic bionic arm.
Fantomex's nervous system externalises itself as a UFO-like techno-organic ship called E.V.A.
New Mutants: The shapeshifting Warlock often turned "him"self into a starship to transport the titular heroes around.
Power Pack: The group had a sapient "smartship" called Friday.
In Alien, there's Mother in the first one and then Father in the fourth. While Mother only talks at the end, to repeatedly warn that engines will overload and then explode, she remains neutral about xenomorph the whole movie, analyzing it like a biologist, or Ash, would. Father seems to take it more seriously, like a soldier, and adds some good manner. Justified as Auriga is supposed to be a military ship, while Nostromo a cargo one.
Father: I'm sorry, access denied.
Father: Non-human presence detected [...] Main vessel declared uninhabitable.
Father: Thank you.
Icarus II, in Sunshine, seems inspired by parts of HAL 9000, Mother and Father.
Nightingale: the titular hospital ship in Alastair Reynolds' short story is sapient. Also, the Nostalgia For Infinity after the melding plague takes over.
Robin Hobb's Liveship Traders trilogy features many living ships (liveships) with sapient, talking, humanoid figureheads. Notable ships include Vivacia, Ophelia, and the mad ship Paragon. Liveships gain their sapience mostly by absorbing the lives/memories of three members of their owning family, at which point they quicken and become alive. Note the "mostly"...
Trader Team: stories center on the crew of the ship Muddlin' Through, largely run by the ship computer, Muddlehead.
The Culture: The Culture's ships are living ships; self modifying, self repairing and with godlike Minds.
Xeelee Sequence: a race of spacegoing, whale-like starships called the Spline, who intentionally modified themselves to be able to survive in space.
Wild Cards: the Takisians use and breed sapient (or semi-sapient) ships. Dr. Tachyon's ship - which he named "Baby" - regenerates its "ghost drive gland" over a period of years or decades, after he burned it out trying to go real fast.
Hyperion Cantos: The Consul's "singleship" is piloted by an AI (and lacks obvious manual controls).
Star Trek novel Memory Prime: introduced the concept that every once in a while, a starship's computer would gain sentience. The mind would thus be moved to the huge computers at, well, Memory Prime, to help support the Federation.
Further explored in the first Strange New Worlds short story Of Cabbages and Kings, where the Enterprise-D, lost in a hostile dimension without her crew, activates a computer protocol to become sentient to survive. After crew and ship are safe, the new A.I. backs itself up into the Minuet hologram.
Path of the Fury: the protagonist steals a Cool Ship that can only be run by an AI that imprints on and merges with the mind of its pilot; she winds up with Megarea, a smart-mouthed and unusually independent version of same.
Remnants: "Mother" is a sapient starship. Unfortunately, after having been abandoned by her creators for centuries, she's also kind of insane.
The Polity: Polity war ships are commanded by AI's and one of the older ships also has a human captain who is wired directly into the ship and in a sense is the ship.
The Walrus And The Warwolf: there is a sapient spaceship that expresses irritation with the pirates on board who are distracting it from contemplating the deeper mysteries of the universe. The pirates think the ship is a flying island and accidentally break its black hole reactor, destroying the ship.
Tuf Voyaging: subverted, where the biological warship Tuf 'inherits' as the last surviving member of a freelance salvage team is specifically NOT sapient, though it could have been made so; there is mention of other Earth warships with AI installed mutinying and/or fighting each other.
The Fall Of The Galaxy: the fleet of the Bargon Empire almost entirely consists of small biomechanical raider ships instead of the Standard Sci-Fi Fleet, which is used by the other major human powers (the Galaxy and the Seven Systems' Union). These ships have proven to be extremely effective at operating both on their own and in small groups to conduct raids into enemy territory and wreak havoc with supply lines and even destroy major targets before jumping to safety. Despite the fact that the ships are crewed, the demands of fast-paced ship-to-ship combat require split-second decisions that are best made by the biomechanical brains of the ships themselves. Normal raider ships with electronic brains have proven themselves vastly inferior to the melding of rapid computer calculations and biological unpredictability.
The Artifact: all Brotherhood ships are cybernetically "alive", Boaz has even managed to become self aware.
"Voyage of the Princess Ark": Dragon Magazine articles: in which the titular Alphatian vessel explores the world of Mystara. Although initially a non-sapient sailing ship enchanted to fly, the Princess Ark eventually fused with a powerful sphinx-like extraplanar entity, acquiring a new layout, the capacity for self-direction and self-defense, and a quirky personality.
Wor Ship by Frank Herbert: after a Generation Ship becomes self-aware, it hijacks the crew and demands humanity learn how to WorShip it.
Empire from the Ashes: Dahak is a planetoid dreadnought the size of the Moon, which attained sentience during 52,000 years of unsupervised operation. Fortunately, given its ability to wipe out star systems simply by FTLing/deFTLing in the wrong place, it's a good guy.
Fluffy from Pat Murphy's There and Back Again is an intelligent space fighter developed as an experiment by the Resurrectionists. Her brain matter comes from a combination of an adventurer and her cat, hence the name.
Greg Bear's Hull Zero Three, in which Ship (AKA the 'Golden Voyager') is heavily damaged and missing much of its memory. But Ship Control, that is, Ship's operating systems, shows signs of incredible creativity. Especially when it comes to the 'Killers', biomechanical servants designed to do exactly what their name says. The narrator, Sanjay the Teacher, realises that the reason why a specific Killer - a Tracker called Tsinoy - has the mind of an astronavigation specialist, is because Ship decided that an astrogator was the most important crew member it could produce, and thus the least expendable. So Ship made Tsinoy a Tracker, able to defend herself and others to the point of near-effortly dispatching two Large Killers at the same time.
The spaceship Heart Of Gold is maintained by Eddie, a Sirius Cybernetics Corporation computer with a sickeningly cheerful and optimistic programmed personality. Other equally unlikable computers have been installed to run other functions on the ship as well, right down to automated doors run by programs that live for the chance to open and close for someone. At one point Zaphod discovered that Eddie had an emergency backup personality - unfortunately, it was worse.
There was also a police ship which committed suicide after talking to Marvin.
In D. Alexander Smith's Marathon series, the ship's computer becomes self-aware during the outward stage of the journey. In the third book, it is revealed that this was entirely intentional. The ship's designer deliberately designed the computer to have vastly more memory and computing capacity than it needed for the mission, all in the hope that it would develop sentience. The computer loves its human charges and does its best to aid them in their mission even while, at first, hiding the fact that it has become sentient.
Nightflyers, a sci-fi horror story by George R. R. Martin. Several crewmembers die suspicious deaths when they start investigating the nature of their unseen captain. Turns out the captain is real, but his misanthropic dead mother is psychically imprinted into the spaceship's system. In the end the captain is killed trying to protect his crew, but in dying manages to imprint himself into the ship as well, and the Final Girl chooses to stay on board to help him fight his mother's constant attempts to wrest back control.
Blake's 7: the starship Liberator is fully sapient but entirely mechanical. In the recent audiobook remake/reboot of the series, the ship is at least partly biological and considerably more sinister, attempting to assimilate the crew into itself and being rather predatory in its attempts to survive.
Lexx: the titular ship is mostly (and often gruesomely) biological. It can speak directly to its crew, and its hobbies include blowing up planets. Strangely enough, it even reproduces at the end of the series, spawning a smaller light-white version of itself when it dies...of old age. Since Little Lexx has no mechanical parts added to the hull or machinery of any kind like the original's cryo-pods and moth breeder bay, it's likely that the non-organic elements were added to the original as it was growing. Little Lexx even has a glowing angler horn.
Farscape: Moya is a Leviathan, one of a species of sentient biological starships who communicate through their bonded Pilots. Her son Talyn, as a hybrid, does not need a Pilot to communicate. Instead, he has a direct neural link to his commander that can be used by any species (presumably.)
Red Dwarf: The AI of the spaceship is represented by Holly, a floating head on a black background that appears on monitors all over the ship. Originally it took the form of a bald, middle-aged man, but switched to a blonde woman before turning back again.
Vorlon ships are at least semi-sapient - they can sing, they're customized to be loyal to their captain, and they grieve over his death and would fall into rage if he was attacked.
The original AI for the Babylon 5 station itself was apparently sentient. It also had an extremely surly and abrasive personality so it was disabled in favour of the basic AI seen for most of the show. One episode had the original AI inadvertently reactivated. It drove the crew to distraction.
Battlestar Galactica (Reimagined): The Cylons of the 2004 re-launch despite being mechanical in appearance, the Base Stars are controlled by a humanoid cylon that is fully integrated into the ship. They're a bit on the "crazy" side though. The Centurions and fighters also have the capability to become sapient, but are intentionally kept at significantly lower levels of intelligence to keep them inline, making them Organic Technology for most of the series.
Battlestar Galactica (Classic): In one episode, Starbuck was assigned to the "Recon Viper", a fighter with more powerful engines at the expense of being completely unarmed. It was run by an AI named C.O.R.A., who acted like Starbuck's pouty girlfriend.
The Doctor's TARDIS in Doctor Who, and presumably all the other ones before they went up in smoke with the other Time Lords. In "The Doctor's Wife", its mind/soul ends up in a human body for an episode, and the way they interact basically makes all the "TARDIS = wife, companions = bit on the side" speculation canon.
Doctor: She's the TARDIS. But she's a woman! And the TARDIS! And a woman!!
Amy: ...Did you wish really hard?
Destiny, from Stargate Universe is somewhat sentient - while it doesn't (usually) talk to the crew, it knows their needs and is very dedicated to its mission.
The Eldar ships combine elements of this and the ghost ship. Eldar souls are stored in so-called Infinity Circuits to save them from being caught, tormented and eventually devoured by Slaanesh. The Craftworlds, the incredibly vast space-faring ships the Eldar live on, are Mind Hives due to the hundreds upon thousands of Eldar minds inhabiting the circuit and the souls often provide advice and information to the living Eldar.
Many Chaos ships are infused with Daemons, in many cases giving them sapience. Some extreme examples of this slowly devour, or even forego entirely, human crew.
Since Tyranid ships are living beings, they are probably sapient due to sheer size if nothing else.
In Mindjammer 2-space ships such as the titular class have to be sapient in order to handle all the minute course corrections needed to avoid the smallest gravity well. Most of the Commonality and allied powers use eidolons, Artificial Intelligences derived from the uploaded memories of deceased people. However the xenophobic Venu Empire hooks human pilots into their ships, which almost always drives the "brainjacks" insane.
Homeworld: The Mothership is actually a Kharakid Scientist, Karan Sjet, who is embedded in the core. She developed the technology to connect a human brain to the Mothership, according to the manual, and she refused its usage on any other person save herself. During gameplay it's her voice who represents the entire ship, along with the spokesman for Fleet Intelligence. It's her image that appears when the mothership is talking. Finally, she's the only named character that appears in all 3 games of the series, and implicitly the Player Character.
Also occurs when EDI's shackles are taken off and she becomes the Normandy.
Since Geth are nothing more than just software at their core, depending on the size of the vessel in question, the number of Geth runtimes housed within might number between a few thousand to over a trillion. They were working to build a Dyson Sphere to house the entire Geth consensus but the Quarians destroyed it between the second and third game.
Sexy Parodius, Vic Viper and Lord British seem to be sapient beings, rather than mere ships with pilots in them. Of course, this being Parodius, this is played up for comedy.
Metroid Prime 3: One of the few games to mention how an intelligent computer can benefit a normally crew-run ship; Olympus-class battleships with an Aurora Unit have cut down on the crew requirements, leaving room for more weapon systems.
Samus' replacement gunship in Metroid: Fusion has an AI integrated into it. "Adam" (named for Samus' CO in Other M, who the AI reminds her of) can't start the ship on his own, but he can do everything else. At the end, it turns out the AI and the original Adam Malkovich are one and the same, via Brain Uploading.
Albion: The Toronto mining ship, NED, the computer operates everything with the crew's main purpose is maintenance or operating individual equipment, and the ship itself is described to function similarly to a living organism, settling on the surface of a planet and using a percentage of the mined materials to grow and eventually cover and exhaust the entire planet.
The Cetans in Perfect Dark are implied to be this, although gameplay-wise, the Cetan ship you explore doesn't really do anything.
The titular ship in Twinbee, along with the other Bee series ships Winbee and Gwinbee, are explicitly sentient in all continuities (this naturally carries over to their appearances in the Parodius series).
In the X-Universe series, the Terraformer / Xenon CPU ships are the hubs of the Xenon fleets. The ships are extremely large, and while their intelligence is simply a bundle of algorithms to start off with, it's possible for them to become self-aware. #EFAA and #DEFF in the X-Encyclopedia are stated to be sapient, but the only CPU ship encountered in the games, #DECA, is not. The rest of the Xenon ships - their destroyers, fighters, corvettes, et cetera - are not sapient.
Every flying unit for the Zerg in Starcraft is both capable of space travel and alive. The best example would probably be the Leviathan, a massive Space Whale like being that dwarfs Battlecruisers.
Beyond Reality: Sebastian is the A.I. for a dimension traveling flying pirate ship.
Freefall: The Savage Chicken will frequently talk to the crew and makes witty retorts. As well as try to maim the captain.
Schlock Mercenary: It's a rare exception when a capital ship is flown by a human pilot or even a mobile robot. Almost every armed starship we see is inhabited by its own AI, who "is" the ship and considers the whole structure its body. A number of them from different factions have networked together and now represent the most powerful independent force in the galaxy. The only ships noted to lack such features are either new, small civilian vessels (and at least one of them has a "synthetic intelligence" which operates some self-preservation routines) or lobotomised.
Zap!: The Excelsior is sapient, chooses its own captain, and is also apparently having an affair with Robot.
Orion's Arm: Has a variety of these, to the point where the only polities that don't have them are virulent human supremacists. The most intelligent ones are non-biological due to the prevailing attitude that meat can only get you past the second Singularity or so.
Red vs. Blue: Sheila, the AI that inhabited the Blue Team's tank before being transferred to a small spaceship. FILSS, who Sheila was apparently based on, is seen in prequel scenes to control the Freelancer ship Mother of Invention.
Starwalker: The ship's AI Starwalker (aka Starry). She uses a holographic avatar of the woman she used to be. AI ships are common in the story but she's unusual in having a personality.
The Last Angel: Nemesis, one of the last remnants of human civilisation after Earth was destroyed by the Compact, is inhabited by the AI Red One. When she failed to protect Earth and humanity, Red One set herself the task of destroying the Compact whenever she came across it. Not an easy task when your enemy is a galaxy spanning civilisation and you have just one ship, which probably explains why she is still at it, 2000 years later.
Futurama episode "Love and Rocket": the Planet Express Ship gets a new AI, which quickly falls in love with Bender.
In Transformers Animated, it turns out that Optimus's team's ship is Omega Supreme, one of the largest bots created in the previous war who can transform into a ship. For most of the first and second seasons, he was in stasis lock (read: somewhere between comatose and dead) and therefore was not sentient until Ratchet revived him with the help of Sari's key.