The actual animation in photoshop is very easy. Think in terms of "cells" in animation, where each cell is a frame of the animation.
Then build layers that contain the cells.
Open the animation window and\ the first frame will already there. Simply add frames and turn on or off the layers in each frame. [frame 1 turn on layer one. Frame 2, turn off layer 1, turn one layer two, etc.]
To make your animation, I made a layer and painted over on of the waves. Then I made another layer and painted over the second wave, and a third to paint over the third wave. Then I duplicated each layer and set the opacity to 50%.
Starting at the bottom of my layers, I had the back ground. The first wave hidden, the first wave hidden 50%, the second wave hidden, the second wave hidden 50%, etc.
Then I made a frame for each layer combination and used the "Save for web & devices" command to save it as an animated gif.
