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The one I've used most is Galv's Layer Graphics.  :)  

okay, thank you, do you have any screenshots of the code?


Here's what I used on one of my test maps:

LAYER_S 4 shadow004 0 0 255 20 0

LAYER_S 5 light004 0 0 128 21 1 0 0

LAYER 6 clouds 0.25 0.25 80 22 2 2 2

I had two stationary layers (shadow and light) plus one cloud layer that moved at an angle (if I remember correctly).  255, 128 and 80 are opacity, so you can adjust those to suit the colors of your map. 

Actually now that I think about it, I have a walkthrough with examples:

I don't think I included info on animating the layers in that, but maybe I did.