By default, Tomboy runs in the Panel area of GNOME, as an applet manually added by the user. This means that it will display it’s own icons and application window.
If you want to make it run in the Notification Area instead, besides the click and keyboard indicator and the rest of the minimized application icons this area displays, run Tomboy with
tomboy –icon &
This will start up the application and nicely integrate it in the Notification Area instead of the GNOME Panel applet area.