With AllTray you can dock any application with no native tray icon (like Evolution, Thunderbird, Terminals) into the system tray. A high-light feature is that a click on the "close" button will minimize back to system tray. It works well with Gnome, KDE, XFCE 4*, Fluxbox* and WindowMaker*. (*) No drag ‘n drop support. Enable with "-nm" option.
Install alltray in ubuntu
sudo aptitude install alltray
This will complete the installation
Configuring Transparent Terminal
First you need to open Gnome Terminal from applications--->Accessories--->Terminal
Once it opens go to Edit--->Profiles
Once it opens you should see similar to the following screen here you need to Press the New button
Once it opens you should see similar to the following screen here you need to give the new profile a name and click on create
The profile editor dialog should open.
Here, uncheck ‘Show menubar by default in new terminals’.
Go to Effects tab, select ‘Transparent background’ and set the transparency amount close to None.
Go to Scrolling tab and select Disabled from the drop-down list.
Close the editing profile dialog and in the Profiles dialog, select the newly created profile from the ‘Profile used when launching a new terminal’ drop-down list of your choice and close it.
Create a new launcher on the Desktop (right click on the background)
Now you need to enter a name for it,insert the following command in the ‘Command’ field,comment field and click on ok
alltray -x -st -g +380+5 "gnome-terminal
Launcher created on desktop as follows
Make sure that one of your Gnome panels has the ‘Notification Area’ applet.Open the launcher created on the desktop and click on the terminal icon in the notification area. You should now have a transparent terminal in your background.
One more Transparent Terminal screenshot