Rearranging hull. During combat or to shift from atmosphere, underwater, or interstellar modes- computer rearranges the mass of the ship for optimal conditions, scrambling the location of everything. Primary rooms and cavities within the ship are mostly kept the same, but crew quarters and other rooms are jumbled and compressed, especially storage lockers and the objects within.
Whenever this is used, you may be trapped in a cavity with one tiny vent to the life support system, as the computer figures that's good enough to keep you alive to make space for its new flight mode or extra large storage bay. Anything vitally important has a 1 in 4 chance to get lost in a really unexpected place.
 Ship AI. It is highly advanced, remembers things, and can fully advise and manage many aspects of the ship. The ship can organize cargo shipments, resupply itself, lock/unlock doors as needed, and many other useful functions. However it is installed with several preset “personalities”, each one having their own problems. There is a kindly grandpa personality which grates on the ears and chides party members for swearing or engaging in effective but dishonorable tactics. There is a sultry female personality which throws mild and temperamental mood swings if not constantly sated with gifts or praise. There is even a highly effective default “factory” personality which works great except it constantly needs to shut down to update and pesters the party to buy it “essentially new features!” straight from the corporate servers.
 Adjusting life support. This life support system is highly advanced, pushing bubbles of air and moisture and customizing rooms based on the inhabitants as they move through the ship. It uses tractor beams to pull around globs of water for aquatic creatures, blasts heat and disperses it just a few inches away for creatures from lava worlds. Aliens of wildly different environments can live here together somehow. However the ship stores the information on its database which could be scrambled or hacked, and occasional hiccups to the system make it send electrically charged clouds of acid smoke for humans to breathe or spraying reptile creatures with liquid nitrogen, since it may accidentally think they need to stay cool due to their temperature being low. Less lethal hiccups, like regulating the inside temperatures and pressure to create weather effects inside the ship are not uncommon when this system fails.
 Replication Engine. The ship has some simple mining/extraction equipment, that can break down scavenged metals and asteroids and use it to create armor plating and munitions. The inside of the ship can be converted to a mini foundry to create and shape these metals and weapons. If left on however, it may flood the cargo bay with dangerous, primed warheads and a single gravity failure in the ship will cause molten metal to float out becoming a lethal hazard.
 Ship-Wide Holodeck. Everything in the ship can be made of solid state holograms; seats, control panels, clothes or personal items, fake crew members acting as visual aids and assistants to the crew, etc. Holograms don't 'despawn' when no longer needed though without supervision; you'll run across historical figures, game simulations, weird sex fantasies and so on running around the ship all the time. If the program is turned off, the control panels of the ship will disappear along with your seats and safety belts; the holograms were aids to assist with the now very inaccessible internal control and machine networks.
 Personal Butler-bots. The ship has a few robots, one per each major crew member, who waits on their every need, cleans up after them, and assist them in their duties. The butlers have all the regular protection protocols and some basic personality circuits; they would never attack the regular living crew members. But they start to scheme against each other, getting in each other way, and stealing each others batteries and server presence to better assist their own personal owner's jobs around the ship. Eventually, they will begin performing combat maneuvers and equipping themselves for gladiatorial combat- your maid bot starts smashing objects to slam the glass into the sensors of a rival machine, who is fiddling with the controls to the airlock to eject the offending robot out into space, and accidentally the rest of the oxygen in the living quarters too.
 Spontaneously generated music played over the projected loudspeakers. Give everyone on the ship a “soundtrack” for their life. Gets annoying fast, even if the music is generated unique and fresh each time. You can ask to turn it off, but it comes back as “subtle background music” in a few hours. You'll get used to it, and eventually go crazy like everyone else. There's at least one crazed naked man in the vents, stuffing his ears with cotton stolen from pillows and sleeping next to the loudest engine machines, just to drown out the music and hopefully go deaf.
 Hologram crew members. After someone dies, they can be simulated and “revived” via a perfect copy of their brain scan and personality from recordings by the ship's computer. Though they are not physical, they are still part of the crew and have the same duties and responsibilities.
Because of this feature, the copies feel as though they got no reprieve even from death, now forced to continue to work and exist in this limited, nonliving state. Also, it is entirely possible for the entire crew to die, becoming nothing more then hologram ghosts in a dead ship they cannot touch.
 Extremely fast acting and easy-access hibernation pods. Metal ports are installed in the back of the neck of the crew members; an easy plug in causes immediate deep, unaging sleep. Crew spread out their lives over eons if possible, taking century long naps along with tiny sleeps of just a few minutes while waiting for their food to cook. Any mistakes in programming and the 'alarm' could be hundreds, thousands, or even millions of years off. With the other crew sleeping 99.99999% of the time, any mistake like this could easily leave the ship unattended and without vital maintenance or repairs for decades.
 Biochemical adaptation. Each crew member has their tools, living space, and even personal needs met with generated biomechanical constructs, created from cloned DNA and shaped into various helpful organisms. Naturally, these beings must be fed a nutrient rich slurry from dispensers around the ship. Once these resources run out, they will become mad with hunger and attack the only meat they can get their hands/claws/protoplasm on.
 Gravity displacement engine. Allows artificial gravity to be selectively altered in real time along different axis; letting you walk on walls, create heavy zones to keep prisoners contained and on the floor, light zones for industry and ease of movement, and so on. Every time the computer reboots or the ship's engines go out the gravity wildly shifts and fluctuates; 1 in 6 chance minor black hole is formed somewhere in the ship.
 Weapon adaptation. The weapons aboard this ship automatically adopt to rearm and calibrate to go past new types of armors and energy shields. Using energy and munitions in an extremely efficient matter. The computer AI always goes for the most powerful method of destruction, and as such the ship starts to become a hazard. Soon asteroid fields are obliterated causing collateral damage, and tether-tractor beams are pulling holes in a friendly's boats hull, just to sate its bloodlust.