If I know the conditions are going to be windy/choppy, I'll start dosing up on Dramamine the night before, continuing with doses every few hours to build up the drug in my system. If ginger tea is available, I'll start drinking that as well. And fresh ginger is great to nibble on the boat, if you can get some.
If I haven't done any of these things and I get nauseous on the boat, I try to stand in/near the center of the main deck where the boat is swaying least, and focus my eyes on the horizon. And if all else fails, I'll just throw up over the side; I hate doing it, but I usually feel better afterward.