Class Skills: Profession is (Wis). This list gives Knowledge and Craft skills not listed in the PH: Boating, Cartography, Navigation, Sea Lore (Knowledge) and Sailmaking (Craft). Be sure to make these available to any PCs who might potentially wish to join this class.
Freeport: The City of Adventure reprints this class (pp. 119-120), adding Jump (Str) to class skills, and changing Knowledge to [local, geography, history, sea lore].
Animal Companion: Note that, per the DMG, p. 46, adventuring characters are usually limited to 1 HD/level. Freeport pirates should be limited to animals which adapt well to ship travel (monkeys, parrots, cats, rats, etc.), which will probably also limit the size and strength of their possible companions.
v.3.5 Update
Replace with the Corsair base class presented in Crisis in Freeport and the d20 Freeport Companion.