Gnome 3 has three separate areas where the same things can go, with a rationale for each: running applications in the dash on the left, system settings in the system tray at the top right, and notifications at the bottom of the screen.
It's not a perfect taxonomy. If a music player is running, why can't you see what it's playing and control it from the dash? Does it really belong in the notification area.
But it's a taxonomy I'm willing to go along with. Gnome users, however (who are revolting) are not. They want to put the program icons, the weather, email notifications, instant messenger chat notifications, music players and probably the kitchen sink back in the panel.
There's a Gnome 3 extension to notify the arrival of emails, but it appears in the panel, not in the notification area, where the new paradigm says it should be. Another email notifier, Mailnag, appears in the notification area, where the paradigm says it should be.
I used it in Fedora, but unfortunately
One problem with the new notification area is that notifications are visible for only a few seconds before either disappearing or being moved to the persistent notification area at the bottom right of the screen, which the user has to actively invoke: if you've popped out of the room to make a cup of tea, you're not going to see that new email notification.
There's another Gnome extension that keeps notifications in the message tray until clicked. But using it means that notifications of transient events, for example a song change, will not behave in a rational way: they will remain until clicked.
The obvious answer would be for some notifications to remain until dismissed (new email, IM) and other not. It will be interesting to see how the Gnome developers respond to the issue. Personally I hope they can find an elegant solution within the new paradigm: I'm not one who is inclined to try to recreate the old system tray in my top panel.