What 3d software are you using?
My first guess might be:
Use an image like this, RGBA where each channel is a cloud pattern, tiling. Then pan them over eachother in a cloudy material in udk. You could then apply that to a tile-able piece od geometry that is an animated wave. Finish that with some alpha cards of whisps to break up the edges.
The very distant clouds could be a horizontal bar of slowly animated clouds. Basically a ring in front of the skydome.
BUT... That is possibly an older and cheaper method. There might be more innovative, cooler ways to pull it off.