I know this is a pretty long-term ordeal, but I think I remember Toady wanting to make elves and humans playable in the distant future, and there was talk of sending parties of units away from your fort's site to go on missions. I think it would add some flavor/specialization to the humans if they were the most proficient sailors, since it kind of makes sense. Elves are more magical than technological and seem content to malinger in their forests, and while dwarves are fantastic engineers I can't see them taking well to being at sea for long periods of time, since the ocean is just a vast, outdoor expanse. Most of them would probably not be very sea-worthy, but their boats would probably be of good construction like everything else they make. I'm imagining a scenario where the dwarves hire out humans to man their ships with a dwarvish captain to oversee them. But that's only one interpretation really, there isn't a lot of canon to DF.
But, I'm probably looking forward to boats more than anything else, the question is what to do with them. Transport for troops and settlers? Exploring parties? Trade ships? Off-shore fishing? What about pirates? Y'arr! Yes, I think boats would be a deep well of possibilities.