The ProLand video linked above is pretty much a verbatim implementation of the usual suspect, which is the Simulating Ocean Water paper by Tessendorf:
NVIDIA covers a compute shader based version of it:
And the shading approach is pretty much covered by NVIDIA as well. It's worth downloading the NV SDK and looking at the OceanCS sample in detail.
The AC3 work appears to be quite a bit more complex, but it appears to still be grounded in the FFT approach. No point tackling it if you don't understand the Tessendorf paper.