The Waves effect has been extended to allow for more natural progression
of waves (logarithmic), and to simulate an object moving through the water
surface.

HOWTO:

 - Create the usual subdivided plane for the water surface.
   IMPORTANT: The water surfaces needs to be at Local Z=0, i.e., at
   the object center. So don't move the vertices 'up' or 'down' inside
   editmode.
   
   Turning on "Subsurf" on the mesh will show realtime lighting too.
   
 - Create an Empty. This will be the boat. (You can use any other
   object, though only the center point will be evaluated, not the
   individual vertices)
   
 - Go back to the Water surface, add a Wave effect, enter the name
   of the Empty into the BoatOb: field
   
 - Turn on X, Y, Cycl, Log, and Boat.
 
 - The "Height" value still determines the average height of the wave,
   but now it is modified by the boat's speed and how deep it sticks
   into the water. If the boat doesn't move, no waves are caused, neither
   if it doesn't touch the water surface.
   
 - "Resolution" determines how many wave simulations per frame are
   calculated. Higher values are more accurate, but slower.
   
 - "Dampfac" is the damping factor of the material for the logarithmic
   ("Log") setting. The higher, the faster the waves decays.
   
 - "Sfra" and "Efra", if set to non-0, determine when Blender starts
   and stops evaluating the effect. This is just meant to speed-up the
   animation preview when the waves decayed enough to be invisible.
   
   The further into time and the more frequently the boat touches the
   water (i.e., the more waves need to be simulated), the slower the
   simulation gets (as it ALWAYS calculates ALL previous frames, too).
   
   Also, Logarithmic waves NEVER *fully* decay - so you can set Efra:
   to a reasonable frame when the material doesn't show the waves
   in render anymore.