I don't know much about water. Marco is working on dynamic water(see Forecast). I don't know how it will work, but maybe you'll be able to apply the wind script to it. That would be cool if it worked right...probably be slow as all get out. You can apply it to the vertices of tree models, but I never successfully coded it. Almost at one point, but slow.

The original C++ version of the script along with the vertices crap is here:

http://edgarapoe.home.mindspring.com/quixotic/blustery_trees.htm

I added a lot of my own stuff to the ported version, but the model manipulation code is there along with an EXE of his version.