Here is a shader i put together recently after reading a bit about what Naughty Dog did for their water in Uncharted 3. It still needs some work on the textures and lighting but it runs well in the maya viewport - 300 fps with an unlocked framerate WOO HOO!
It features my implementation of Gerstner Waves combined with vertex color flowmaps, allowing you to control the direction of both the vertex and texture animations. Its also crazy cheap for the motion you get, so it is an ideal technique for games. I'll probably port it to a game engine like Unreal or Unity once i figure out what i want to do with it :)