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Quick tip for Firefox users: GNotifier is a Firefox extension that makes the browser use native notifications on the Linux desktop. The extension currently supports GNOME (Shell), Unity, KDE and Xfce.

Below you can see a Firefox notification in action using GNotifier, under Unity and GNOME Shell:

Native Unity notification Firefox

Native GNOME Shell notification Firefox

Besides regular notifications, like the one displayed when a file is downloaded, the extension also supports the standard webkitNotification API (for instance, receiving notifications on new emails in Gmail) - to use this feature, Firefox needs an user script like THIS (you'll need Greasemonkey extension to install user scripts).

Get native Linux desktop notifications in Firefox with GNotifier

To install GNotifier Firefox extension, visit its page and click "Add to Firefox": GNotifier @ Firefox Addons.

The extension should start working immediately, without having to restart the browser.