When you set the panel to be transparent in the default Ambiance theme in Ubuntu, you will find that some panel items' backgrounds are not transparent, but you can make them transparent and consistent with others, following these steps:
- Go to Applications (or Main Menu) > Accessories > Terminal.
- Enter cp -R /usr/share/themes/Ambiance ~/.themes/
- Enter gedit ~/.themes/Ambiance/gtk-2.0/apps/gnome-panel.rc (for Ubuntu 11.04 or 10.10) gedit ~/.themes/Ambiance/gtk-2.0/gtkrc (for Ubuntu 10.04), to open the file with gedit.
- Search for this line bg_pixmap[NORMAL] = "img/panel.png" (for Ubuntu 11.04 or 10.10) OR bg_pixmap[NORMAL] = "panel_bg.png" (for Ubuntu 10.04)
- Comment out the line by placing a # at the beginning of the line, like this: # bg_pixmap[NORMAL] = ...
- Save the file.
- Go to System > Preferences > Appearance, switch to the other theme and then back to the Ambiance theme.