Shipboard Roles

Captain

The captain is in command of the ship and is the final authority while aboard it.

First Mate: Navigator's Tools required. The first mate is the captain's right hand, and a commanding officer. The mate's orders are law, save when they conflict with the captain's.
Navigator: Navigator's Tools required. In charge of plotting courses, usually in conjunction with captain and/or first mate.
Quartermaster: The quartermaster is in charge of overseeing supplies and the morale of the crew. They often bear the keys to the paychest along with the captain, and usually handle the ship's books as well.

Boatswain: Vehicles (Water) required. In direct charge of the deckhands, the boatswain (usually slurred to "bosun") oversees rigging and cargo handling while in port.
Bosun's Mates: Vehicles (Water) required. The two subordinates of the boatswain, who take on his responsibilities while he is off-duty.
Helmsman: Vehicles (Water) required. A member of the crew assigned to man the ship's wheel. This isn't a permanent position, but is one assigned on a by-duty basis, from among senior deck crew. The helmsman answers only to whatever conning crew are on-duty at that time.
Deckhands: Members of the crew assigned to the deck.
Rigsman: Members of the crew assigned to the rigging.
Lookout: A member of the deck crew assigned to a perch either in the rigging or in a crow's nest, scanning the horizon for ships, land, and other sights of interest.

Master-at-Arms: Crewman responsible for keeping order among the crew and supervising the ship's armory. If the ship carries marines and artillerists, they answer to the master-at-arms.
Artillerist: Crew responsible for manning artillery such as ballistae or catapult. Under the command of the conning officer on duty when in battle, or the master-at-arms outside of it.
Marine: Fighters.

Ship's Mage: Though not all ships have them, many ships employ a wizard or other arcanist to use their magics to the benefit of the vessel.
Chaplain: A shipboard priest is common with larger ships, although they also usually fulfill another role in addition to ecclesial tasks.
Surgeon: A healer (magical or otherwise) is a necessity for even smaller vessels (though on smaller vessels they might also tend to other duties as well).
Cook: A ship's cook is a necessity on every vessel, and in larger ones, there may even be a few of them. Many ship's cooks are those sailors too old or too scarred to tend to other, more physical tasks any longer.