Any advice for running a Swashbuckling Sea-going Campaign?

[Bauglir]

On the crunchy side of things..

Beware of sorcerers in ship to ship combat. I've seen a sorcerer devastate a ship by volleying first enlarged, then normal fireballs over huge distances (remember that a 10th level sorcerer can chuck an enlarged fireball 1600 ft), then flaming spheres once they got close enough (these rolled down below and caused havoc with the cannons and their powder supplies..)

You may wish to tone down evocations in general, or come up with some practical method how it would be handled in your world. (Magically treated wood to make it more durable and less flammable might be a good start, although that still doesn't stop them putting dirty great holes in your sails)

Then there's spells like wall of force and blade barrier at higher levels, which can make short work of a ship.. (stick one in front of a moving ship and soon you'll have a sinking ship..)

 

[The Little Raven]

This is from my experience running a seafaring campaign.

Get to the know the underwater combat rules very well. Also, if two ships are fighting eachother and attempting to ram, or move parallel for boarding, treat them similar to flying creatures with their maneuverability. It's a little more realistic.

Check out the new DMG's rules for fighting in shallow water (such as on a leaking ship).

Require Balance checks for more than a single move action until they get their sea legs.

Don't forget Concentration checks for spellcasters on rough waters, especially with heavy rains at sea.

Climb checks for going up rigging, and a +1 bonus to attack for fighting from higher ground.

Allow Reflex saves for characters that go over the edge, so they can climb back up on their next turn.

Most importantly... have fun.