Web Screen Saver for Joomla form JosXP.com, is a very useful Joomla module, it acts as any regular window screen saver.

Once you install mod_webscreensaver you can change the animated logo by replacing the file [Joomla Home]\modules\webscreensaver\ss1.gif by your transparent GIF file.

From the "Site Modules" you can change the Wait Time to launch the screen saver, the "Delay" to move the logo, the Opacity of the background and the Logo Size.