I'm not sure I follow what you mean but my gut feeling is that you're underestimating greatly the scope of such a task. Have a good hard think about how many games actually use tech like this and not just surface decals ;)

For normal waves take a look at the water shaders available in Unity Pro for a non dynamic effect.

To get the plane to react to other objects in the scene and create "dynamic waves" is not really a simple problem. You will need to edit the verts in the mesh against a clever wave algorithm most likely using the contact[x].point's from a sphere cast.

This will be expensive as hell, as you will need to use a mesh collider to get the points you need. I'm not even 100% sure if mesh colliders will update automatically if you change the shape of their respective mesh.

The mesh class you will need:

http://unity3d.com/support/documentation/ScriptReference/Mesh.html

The collision class you will need:

http://unity3d.com/support/documentation/ScriptReference/Collision-contacts.html

A better route to take here would be to combine a non-dynamic effect with an animation model to show water displacement and blend that to decals maybe for wake.