Does it actually ripple? It's so realistic looking that I wonder if you're using some sort of fork of FS2_Open with per-pixel lighting or something.
You mean the shaders? Normal maps and such?
Because, you know, that's what they are. Per-pixel lighting. Or pixel shaders, which are what graphics cards use for creating real-time per-pixel lighting effects.
I think it is possible to use animated normal maps which means you could simulate a group of waves interfering with each other, then create normal maps from the water's surface elevation map and voilà you get pretty realistic looking waves. I think that's how it's done in IL-2 Sturmovik, incidentally. You just need a good wave texture with not too obvious tiling and high enough resolution (the tiling is visible in some cases on IL-2 but most of the time it's bloody awesome looking).
Then you could of course add a semi-transparent water diffuse texture and a bottom to the body of water, and craft the bottom texture so that on shallow water you would see the bottom...