For the Ubuntu heads, did you have to download a theme to enable transparency effects? I remember it being a pain in the ass to enable on gnome desktops while KDE was much more user friendly.
What are you using? Gnome2, Cinnamon, Gnome Shell or Unity?
Cinammon/Gnome2
Change opacity tab on panel and terminal properties
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Gnome Shell/Unity -
Easiest? Find a transparent theme on Gnome-Look or DeviantArt
Harder? Edit css file for your particular theme and search for background-color. Comment out and replace with "background-color: rgba(0,0,0,0.9);".
Example: By default, the Bottom Panel extension for gnome-shell isn't transparent. I had to edit the css file manually to make it transparent.

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