Basic ship commands:
Launch - launchs the ship
Shields - toggle shields
Speed <num> - Sets the speed of the ship to num, or the max/min value, ie speed 100000, will set the ship's speed to the max, speed -5000: sets speed to 0
Target <shipname> - target a specific ship to prepare to fire at
Autotrack - will allow you to follow a targetted ship unless they jump into hyperspace
Calculate <starsystem> <x> <y> <z> - Prepares your hyperdrive to jump to starsystem at cooridinates x y z
Hyperspace - intiates the hyperdrive
Course <x> <y> <z> - Sets the course of your ship to x y z, usually done once you are trying to move within a starsystem to get to a landing area
Status - Shows the status of the ship
Open/Openhatch <ship> - Opens the hatch on a ship, you must own the ship, be a pilot or be using a public ship
Close/Closehatch - Closes the hatch on the ship once you have boarded
Board/Enter <shipname> - Allows you to board a ship, only after the hatch has been opened
Link - Allows you to link your weapons systems together, examples "link primary", "link secondary", "link launchers", or "link all"
Fire - Fires lasers by default, or all linked weapon systems at whatever ship is targeted
Fire missile - Fire m, for short, will fire a missile at whatever ship is targeted
Fire rocket - Fire r, for short, will fire a rocket at whatever ship is targeted
Fire torpedo - Fire t, for short, will fire a torpoedo at whatever ship is targeted
Fire chaff - Fire c, for short, will launch a chaff missile which will thwart incoming missiles/torpodes
Fire ion - Fires an ion blast at whatever ship is targeted
A few notes:
Some of the larger ships have navigation rooms, which only naviation things can be done ie: course, calculate.
Some ships have turrets or gunner stations, in which only things such as target, and fire can be done.
I know I forgot some, but those are the basics of the ship system, I think.