Well, what is the background / reason for the voyage?
Maybe the continent the PC's and the NPC''s came from is destroyed / wracked by war. The PC's are not just travelling on a single ship, but a vast armada, from warships and large trading cogs to smaller vessels, anything that floats, is escaping the devastation and trying to reach new land. Plenty of adventure ideas:
- power struggles by military / priests / merchants / nobles on who is in charge of this chaotic operation
- with so many people, old feuds can be an issue: think murders
- food will be an issue; people will be stealing from eachother to stay alive
- expeditions need to be sent off to check where the new continent is
- the usual (pirates, sea monsters, storms etc.)
- some religious nutcase starts a new religion based on the flight, he blames one powergroup for all the problems and tries to set up the rest of the people against them
- along with 'people' many monsters also flee, some in disguise (polymorphed dragons, dopplegangers etc.), others in their own vessels (ships filled with goblinoids and other moenstrous humanoids) which may lead to clashes
the list goes on....