This is a big deal in Windows 7. The problem is that Microsoft itself  was the biggest offender in this area. When I saw the MSN messenger doing the special balloon popup for the first time I was impressed with the quality of it. I did not realize at the that there would not be central place to disable such popups from all of the applications that do this.
I am able to disable all balloon popups from MSN messenger, Outlook 2003/2007 and such from the applications config. I completely stopped using Yahoo messenger after trying to stop it doing that popup thing for a while. These days I don’t even go there. No more yahoo messenger and toolbars for me.
Now the question is, with this positive initiative, how is Microsoft going to get everyone to use a centralized API? Every frigging application and service use their own way to display balloon popups. Some examples are Virus Scanners, Firefox, wireless driver applications, desktop search stuff all in addition to Microsoft software.
Good luck with the effort 