Deck
Regaldes of the size or type, each ship has a deck.
Gangplank
The gangway which all ships come with can be upgraded so that it is sturdy enough to be extended when the ship is not anchored. This permits any golems on board to force undesirables to walk the plank. From silverlake for ~50k gold.
Landing gear
Once your ship has lift magi and is able to fly, you might find it useful for it to be able to land. Landing gear gives your ship the ability to set down nearly anywhere it can get to. From Silverlake for ~105 gold.
Rescue equipment
Rescue equipment can be added to any class 2 or better ship, enabling the officer at the helm to have people outside the vessel pulled onboard after a brief wait. From silverlake for ~38k gold.
Ship's bell
Usually a ship's bell is used to signal other ships its location in mist, as a call signal for food break, for a shift change, to notify certain moment of time, for alarms and to get all hands on deck. However it has also one practical use and it is the ability to bell everyone on board or use *bell in an cruise command to notify the players that the destination has been reached. From silverlake for ~25k.