I use PTAssembler to align the images, then output a layered PSD file and then manually blend the layers together in PS by airbrushing the layer masks. By moving the blend boundary around and adjusting the feather of the blend via brush size and hardness, you can usually match waves and ripples and suchlike fairly well. But as pointed out, it's a painstaking manual process and there's simply no other solution.
I shoot from left to right, so that looking at the images in Bridge shows them in correct order.