I am rather partial to The Seafarer's Handbook from Fantasy Flight Games. Although it is 3.0, it is still a very good reference on seafaring campaigns.
It covers, among other things, aquatic combat for land-based creatures; aquatic PC races; aquatic equipment; and ships.
The section on ships contains a stat-block format for ships, rules for designing custom ships, several pre-designed historical and fantastic ships (one ship is based on the design of the Monitor, an Ironclad from the US Civil War, for example), and rules for handling sea voyages (especially the hazards of such voyages, like fire on the ship). Ship-to-ship combat, boarding actions, and such are more lightly discussed, but present. Feats suitable for a seafaring campaign (such as Swing-by Attack, for those rope-swinging types) are also present. The Prestige Classes are generally limited to one per new PC race presented, and are all aquatic. A few aquatic-based spells are included, as well as some notes on modifying land-based spells.