When the Gmail Notifier emerged from its cocoon last August as the Google Notifier, the utility bizarrely introduced its own popup alerts for new messages instead of simply using Growl, which is arguably the standard in Mac OS X notification systems.
I don't know how we missed it, but Gmail+Growl stayed right in stride and released a 2.0 version to work with the new Google Notifier (in which case, shouldn't this be called Google+Growl?).
As long as you shut off the built-in alert system in Google Notifier, Gmail+Growl works well with the new utility. The one quirk I've found so far is that it doesn't seem to be pulling images from Address Book, and I don't know if this is a problem on my end or an update is in order. Either way, if you prefer Growl for all your system notification needs, Gmail+Growl should fit the bill just fine.