You could try making a wake terrain, then altering it through keyframes to produce a rippling effect? Then link the terrain to the back end of whatever is causing the wake and see how that looks.

It may be easier to make the terrain height map using Gimp or something - I expect you'll get better control over the ripples that way.  You'll probably need one for each side of the wake too.

Not that i've tried any of that : )