You'll want to keep this life ring, or one similar to it close to you until you get your sea legs.  As always the horizon is off afar.

Commands and Aliases

Regular, Captain-only, and Combat Commands. Along with tips for making aliases for quick actions.

Basic Commands
ship board (direction or ship name)
--Ye can't sail if you're not aboard.

ship exit [(direction)]
--Ye can't adventure all the time while on your ship.

ship info
--Shows all the information you need on your ship, save for the cargo manifest.

ship scan
--Grants you a birds eye view of the nearby area atop you crows nest.

ship lookout [('all')]
--Shows your nearby ships and sea monsters.

ship cargo
--Shows your cargo manifest, the items and their quantity and weight.

ship yardinfo
--If docked, shows you pricing information for the current shipyard.

Movement Commands
ship direction (direction name)
--Orients your ship to sail in a certain direction.

ship speed (speed)
--Selects the speed at which your ship will sail; stop, slow, half, full, flank.

ship engine (engine type)
--Ye can power your sail under either sail or steam.

ship rigging (rigging type)
Normal, Weather, or Combat. Weather is currently not needed and it also halves your speed, and you need combat rigging to battle.

ship course list
--Lists all of the marks you currently have for your ship.

ship course set ('course name' or number)
--Sets your ship onto a course to reach the specified mark or course.

ship course cancel
--Stops your current course.

ship course reroute ('course name' or number) (route #)
--Reorganizes your ship marks to string a new course together.

ship anchor
--Anchors your ship in shallow waters. Can only be done at stop or slow speed.

ship mark add (route #) (location name)
--Creates a mark at your current location.

ship mark remove(location name or number)
--Removes a specified mark.

Combat Commands
ship target [(ship or sea creature name or number)]
---Targets the specified ship or monster. If no new target is specified, this command will show distance and health information of the target.

ship target attacker
---Targets the ship attacking you!  Simplifies hunting pirates when many are close by, and might also work for SPK.

ship weapon [('uninstall')]
--A useless command, only a foolish captain would uninstall their weapons!

ship weapon priority (weapon)  #
-- This allows you to just 'ship fire' if you have set a priority list for the weapons to fire from.  10 is the highest, down to 1.  Then zero never allows that bank to fire.

ship fire (weapon bank name)
---Fires the specified weapon at your target.

Other Captain-Only Commands
Ship Officer (name of person)
--Designates someone aboard your ship as an officer capable of helping you command the vessel.  If killing Pirates, both of you will split the experience points.

Ship cargo dump (cargo resource type) [(amount)]
--Dumps an amount of cargo overboard. If no amount is specified, all of that cargo of that type is dumped.

ship salvage
--Salvages any floating cargo in a room. Currently only used for debris from SPK'd ships.  Pirate ships will drop some ammo, and gold-ingots which can be sold back at port.

ship christen (ship title)
--Only used once, but names your ship.

ship plank (victim name)
--Ostracize a passenger off of your ship! Feed them to the fishes!

ship locate
--If you've lost your ship use this command at a shipwright and you'll have its coordinates given to you.

ship repair
--When at a dock, workers will restore your hull and shield to full strength for a small fee.

ship refuel
--When at a dock, workers will refuel your ship for a small fee.

ship drydock
--For a small fee, your ship will be put in storage at that dock.

ship recover
--If your ship has sunk, a shipwright can raise it from its watery grave.

ship launch
--Removes your ship from drydock.

ship contract [(number of crew members)]
--If your ship doesn't have a full crew, you will contract the remaining number from the current dock.

ship transfer (character name)
--Gives ownership to another player of your ship. There is only one captain for a ship.

ship flag (flag name)
--If you have a flag mount, you will fly the specified flag.

Ship Aliases

Typing in some of the ship commands can be very tedious. Convenience in entering commands can be gained by using client or in-game aliases. Speed is only truly necessary with the combat commands, but is useful in all the other commands.
Use short words or abbreviations, no longer than 5 or 6 letters. Below is a list of the aliases that I use. Build off these examples if you wish.
They can be used with the in-game aliases, but some of the multi line aliases I use from my client.

Movement Aliases
sd - ship direction
ss - ship speed
sa - ship anchor
sc - ship course
scs - ship course set
scc - ship speed stop & ship course cancel

Misc. Aliases
sb - ship board
shc - ship scan
shl - ship lookout
shcg - ship cargo
shrn - ship rigging normal
shrc - ship rigging combat
shv - ship salvage

Combat Aliases
sht - ship target
shta - ship target attacker
shfb - ship fire basic-cannon
shfm - ship fire medium-cannon
shfc - ship fire heavy-cannon
shff - ship fire fire-launcher
shfh - ship fire harpoon
shfl - ship fire light-ballista
shfb - ship fire heavy-ballista