Gmail Notifier (which we've covered before) is a great way to integrate Gmail into the Ubuntu desktop as it makes use of libnotify and the indicator applet in Gnome.
The latest Gmail Notifier (1.7.1) was just released and it only comes with one new feature but which many have been waiting for: Gmail Notifier now supports Google Apps email accounts (Gmail for custom domains).
You can download Gmail Notifier 1.7.1 @ its website (Ubuntu .deb).
You can also use Desktop Webmail to set Gmail as your default mail application in Ubuntu.