Some people like Ubuntu's Notify-OSD deamon, because black bubbles are good looking; but in everyday's life, these are so intrusive that it becomes really anoying.
Browsing the internet, I found some a nice blog post linking to gnome-stracciatella-session. This ubuntu package was done to get rid of all gnome ubuntu modification, it contains a single xsession file which runs a vanilla gnome, getting rid of Notify-OSD, reverting to gnome default notification-deamon.
All you have to do is install this package :
sudo apt-get install gnome-stracciatella-session
Then, to use it, when selecting your session with GDM or KDM (or any other login screen), just select GNOME (without Ubuntu specific components) to login and set it as your default session.
Note : This will work with Ubuntu 9.04 release and higher.
Some links and sources :