The great thing about growl is that it provides one central place to control notifications, adjusting their parameters with fine grained control. If you find some particular type of notification obnoxious, change its behavior or turn it off.
If growl didn't exist, every application would provide its own mechanism for notifications, and the user would be left turning off distracting crap in 10 places instead of one, and unable to adjust that one vital notification to behave as desired.