Part II
Sea Gypsies in fleet of small house boats
Sea Gypsy village built out of raft of derelict ships
Angry sea god blows ship 10d10 miles off course
Pride of sea lions (the half-fish half-lion kind)
Questing triton paladin mounted in giant sea horse seeks information
Slave ship taking cargo of slaves to sell
Convict galley of nearby nation
Small fleet of slaver galleys. Will not attack if the ship agrees to turn over 2d6 members of the crew to be slaves.
Large warship transporting VIP (patriarch/matriarch of major religion, member of royal family of important nation, famous archmage, etc.)
Boarding party of aboleth thralls
Afanc
Small sandbar/reef/rock, too small to be on charts. Boat may run aground if night unless skill check is passed. If day, a marooned sailor is visible hailing the ship. He's a one or more of pirate/mutineer/trouble maker/heretic/dangerous shapechanger/sea captain victim of a mutiny/framed for a crime he didn't commit/outcast/drunk/siren or dangerous fey using glamor to disguise true appearance so as to lure boat close enough to attack.
Pack of sea wolves
Scrags
Giant Octopi
Kraken
Mosasuar
A quadrone/movanic deva/ghael/coutl/gynosphinx attempts to land on the ship. It warns the ship that terrible danger lies ahead, and gives them directions that takes them two days off course. If the warning is not heeded, the automatically have a random encounter after one day of travel with 2 times the normal number encountered or with all DC's of skill checks and saving throws increased by 5 (as appropriate).
As above, but the creature is not what it appears to be, and the warning is likewise intended to steer the party toward some hideous hazard they'd otherwise avoid either out of enmity to the party or else a desire to profit from the wreck of the ship. The creature is actually an evil wizard using illusion or shapechange magic, a fiend wearing a false face, a rakasta spell caster, an evil siren sorcerer, a CE genie, etc.
A mated pair of small drakes lands on the ship's mast and begins making a nest.