Heres a simple screencast for setting up Eclipse (or any window, actually!) with a transparent background in Ubuntu with Compiz. Its time to actually enjoy your wallpapers!
One of the great things about Compiz on Ubuntu is how you can control the animations for your windows. So when a window closes or opens or minimizes, you see a cool effect like having the window blow up or burn up or turn into a paper airplane! This is how you can set that up in Ubuntu with Compiz Fusion: