Current desktops support a "notification area", which is essentially a clone of the Windows "system tray", and is almost never used for notification because it doesn't let you indicate a useful amount of information. I'd rather see a cross-desktop notification system that'd look something like Dashboard: a (concealable) large area which could display messages like "New mail from John Smith".
D-BUS could be used as the communication mechanism; messages could include IDs intended to avoid duplicate notification, and the panel could send a notification back via D-BUS when a message is clicked on.
Miguel de Icaza had the same idea: GNOME notifier. It's been implemented as libnotify and notification-daemon.