[afb]

I'm guessing you were not using Adium, which is what I use for IM, since it does change the dock icon for new messages and is a rather good app all around. It also though has an overkill Growl implementation, but at least it gives you the choice. I don't know think it has the option, but Colloquy (an IRC client based on the excellent irssi) has options to display Growl windows only if it's not in front, which alleviates the matter.

In short, Growl itself doesn't really do much; it's up to the app to make good or bad use of it.