Earlier this year, I score two of those killer sailing vessels that WizKids made for D&D. Now I have armaments so they can go on the attack or defend themselves from pirates and evil navies (Pan Tang quickly comes to mind!).
First up is the catapult, the artillery of choice since the Ancient World until gunpowder was readily available. Feel free to chime in if you know but the earliest culture I can recall to utilize catapults would be the Romans. Maybe the Persians or Egyptians did. I would rule out the Greeks initially due to their home turf being too rocky so infantry (hoplites) and light cavalry were more practical. These will have to be on the top deck to be practical against any foes my players encounter.
Pathfinder has the Gunslinger class in 1E which would allow these puppies onboard. Cannons will work well in the first lower deck of my ships because there are portholes to fire these from. Even if my Fantasy campaign has limitations on gunpowder, cannons could still be used as a magical focus or special item that fires lightning, icicles, compressed water and obviously everyone’s favorite offensive spell…fireball.