Getting Started
If you haven't installed the Gimp on Ubuntu 11.10, you can do with this command:
sudo apt-get install gimp
Then open the terminal and edit the panel-border.svg image file with this command:
sudo gimp /usr/share/gnome-shell/theme/panel-border.svg
Under the "Layers" section, move the opacity slider to the left to make your image transparent. For full transparency, move the slider to zero. For my part, I will adjust it to 20.
Save now your file and rename it as panel-border.png since Gimp doesn't support svg files.
Edit now the gnome-shell.css file with this command:
gedit /usr/share/gnome-shell/theme/gnome-shell.css
Search and replace:
panel-border.svg
to
panel-border.png
Save your file and exit. Log out the current session and log back in. Your Gnome Shell panel is now transparent.
Source: http://www.upubuntu.com/2011/11/how-to-make-gnome-shell-top-panel.html