Alien Sea: The Neath does not follow all of the same physical laws as the Surface, and its zee is coloured between black and green.
An Entrepreneur Is You: It might not pay so well as exploring distant kingdoms or hunting pirates, but most captains will spend at least some time ferrying goods and passengers between ports.
Ascended Meme: Ratsending. One player began using Fallen London's basic gifting system to send the lead dev thousands of rats. The mythos of transported rats expanded by degrees; a Pneumatic Ratsender is now available as a ship component.
Call a Hit Point a "Smeerp": Your ship's stats are all named for Fallen London's mysterious rulers, the Masters of the Bazaar - Iron for attacks, Mirrors for observation and illumination, Veils for speed and concealment, Hearts for healing and morale, Pages for knowledge and diplomacy.
Church Militant: Abbey Rock, the coastal convent-fortress of the martial Sisterhood, and Godfall, home to the boisterous pirate-monks who follow the ways of "St Stalagmite."
City on the Water: The New Khanate's cities are variations on this style: Khan's Heart and Khan's Glory form a stately City of Canals on a series of artificial islands, while the other side of the Enemy Civil War, Khan's Shadow, is a colossal assemblage of ships roped together.
Contest Winner Cameo: A number of Kickstarter backers appear in-game as crew, secondary characters, and the names of geographical features.
Cool Boat: Several, including the trimarans of the New Khanate; the partly-organic Cladery Heart; the submarine Irrepressible, with its irrigo-cannon and breakfast-pit; and the dreaded Tree of Ages, crewed by giant spiders.
Darkness Equals Death: In a similar system to Amnesia: The Dark Descent, extinguishing your ship's lights can help you hide from enemies and creep past zee-monsters without waking them, but the darkness prevents you from navigating or seeing foes clearly and drains your crew's Sanity Meter.
Honest John's Dealership: Leadbeater & Stainrod are the Neath's largest, cheapest, least reliable provider of ships, ship components and ship repairs. It's entirely possible that they actually want you to drown.
I'm a Humanitarian: Always a risk when lost at sea, with limited supplies and a cook who's going quietly insane.
Living Ship: The Cladery Heart, a colossal, living heart, clad in iron and set to sea.
Macrogame: When a game ends, the player can begin a new game with their previous captain's maps, one of their officers, or a boost to one of their skills. Wealthy captains can also write a will, allowing their house and some of their wealth to be passed on.
Mad Artist: The Set, a group of highly eccentric and vicious artist-pirates.
The Mutiny: A ship's crew may mutiny against their captain if Terror grows too high. If they can't be talked down or beaten down, game over.
Nautical Folklore: Zailors are superstitious folk, and it's a foolhardy captain who neglects their traditions. Harming zee-bats is unlucky, stones falling from the roof are unlucky, smooth black water is unlucky, asking questions about pigs is unlucky...
Ocean Madness: It has less to do with the fact that the zee is inherently maddening and more to do with the fact that it is dark, monster-infested, and prone to rearranging itself, but Terror will be your constant sanity-draining bane,
Purely Aesthetic Gender: As is standard in Failbetter games, the Player Character can be male, female, or fit any of a number of other descriptors, without limiting their stats or even their portrait.