From Birnam Designs Wiki

To adjust the X window transparency/opacity in linux, use the transset command. If you don't have it already, sudo apt-get install transset should do it.

Examples:

transset 0.5

This will cause the cursor to change to a window-select cursor, the opacity of the selected window will change. Opacity is a number between 0 and 1, but for pete's sake don't set something to 0.

There is also the transset-df, which has some improvements such as the ability to pass the target window by ID through the command line.