I've seen rippling water-type surfaces done with softbodies and I think radial and/or air fields. The fields were parented to the object passing through.

Also, MAYA's built-in water texture has riple settings. You can layer a few of them one over the other with a plus-minus-average node that plugs into the material's bump map. I've tried this myself once and it's pretty cool. It takes some doing to animate the timing of the ripples if there ara a lot, but I'd hazard a guess that it's more controllable than softies and is a quicker render too. Downside: the surfaces doesn't actually deform.