I'm using some of the code from TestIsland and I can't figure out which part of it is making the ripples in the water move. Anybody know?
My guess would be the actual shader does! so, no code in jME does it. 
the movement of the textures used for the waterripples(normalmap and dudvmap) is done in the shader, but based on the variables normalTranslation and refractionTranslation. those are updated in the waterrenderpass dorender method adding speedReflection * tpf and speedRefraction * tpf every frame… speedReflection/speedRefraction can be set with setSpeedReflection/setSpeedRefraction… maybe this is not flexible enough for you though so you might have to hack the shader in that case…