Well, appearently an application uses Growl to send notifications.
There are different applications running silently in the background of the MacOS X System, like the helper apps and certain support apps.
So the first step is to move to the System Preferences - Users and check the startup applications. Well, if there are some old remains or an application which uses growl to send notifications - we need to move to the preferences of the application and disable notifications in the application preferences. GeekerTool is a very well known applications, as well as dropbox is.
Both can work without growl - so we need to change the application preferences.
Also some old dashboard widgets might use growl as notification help. We need to check those also.
Check for old dashbard widgets by removing those, and check if the widow reappears... if not, we've found the widget - and can look if there is an update...
In my case it was an old alam clock dashboard widget - which sends out notifications. I removed it, and the window disappeared forever....
Hope this helps you