i don't like eye candy. compiz, wobbly windows, shadows, fading, taskbar previews; they all just annoy me. i want my computer to do what i'm asking it, and now. i run a slightly minimal desktop, with just openbox to manage windows, a gnome-panel for tasks and systray, and nautilus to put files on the desktop
despite this approach, proper window transparency is a useful feature. i spend most of my work day going between a terminal and configuration files, so it is good to have a semi-transparent terminal in front, and the file i'm working on behind, that i can read off (yes, two monitors would be more useful). how can we get this effect, without all the other useless cruft?
enter xcompmgr. this useful app handles compositing, without replacing the existing window manager. install it with sudo apt-get install xcompmgr, and run with just xcompmgr
start up a gnome-terminal (or stjerm), and set transparency to about 80%. move that window over some other windows or icons, and enjoy actual proper window transparency!
xcompmgr can also do drop shadows, and combined with transset, can be setup to make your windows transparent too. i'm not so into this, but there's a good summary on urukrama's openbox guide