Water has been on my wish list since the beginning. After Googling on a Friday night I stumbled upon Habib's Water Shader Wiki. Habib took the time to put together, write and explain in a very detailed and clear way a great way to render water. Thanks Habib!
This made it possible for me to add water to the sim in about a (long) weekend of coding. If you would like to know the inner workings: I pretty much followed Habib's guilines, so you can read it there. There is still a lot to be done before the water can be included in the next release. For example the Aircraft Editor needs to be expanded to support this new ability. I would also like to let the wave direction and amplitude depend on the wind direction.
Here is a short video of what the water looks like and how it behaves in the sim: