So you have Google Notifier and you're unhappy with that "new message pop-up" window announcing your new mail or calendar events. How do you change it? Simple: you install Growler for Google Notifier (a plugin for Google Notifier).
Growl notifications are small windows showing some text. Out of the box, Google Notifier shows its own pop-up and doesn't sends out those notifications, but Growler for Google Notifier helps Google Notifier send Growl notifications instead. Because you can pick between a variety of Growl displays, your notifications can look pretty much however you'd like. And Growl notifications are sent out by other applications as well, so everything can look consistent.