The problem with GAfYD (Google Apps for Your Domain) is that a lot of the available add-ons, such as the Google Notifier and various Greasemonkey scripts, don't work with the Google apps that are hosted on your domain. Fortunately, however, this hangup is changing.
A new widget called g4me is adding to a slowly growing pile of 3rd party add-ons (such as the private beta Spanning Sync) that are compatible with GAfYD. This widget can check Gmail on your domain, complete with Growl integration for new message alerts.
With Google's recent commitment to the Mac OS X platform, it will be nice to see more solutions like this coming from the big G and 3rd parties alike.