To make individual window transparent on Ubuntu you will need to install transset or transset-df from repository. Note that you have to be running a compositing manager i.e. Compiz for this to work.
To make a window transparent:
$ transset-df -c
Now click on the desired window
This will make your window 75% transparent.
To reset back:
$ transset-df -c -t
Now click on the desired window
You can additionally get more options in the command by invoking -h for help.
