Ubuntu Jaunty has gone completely overboard on the new notifications mechanism. I get pop-up notifications constantly and they make it really hard to concentrate on anything for more than 10 minutes. I finally had to disabled the notifications since they were so annoying. If you want to disable the notifications in Ubuntu Jaunty, you can do so by opening up a command line and entering the following command:

sudo mv /usr/share/dbus-1/services/org.freedesktop.Notifications.service /usr/share/dbus-1/services/org.freedesktop.Notifications.service.disabled

Once you execute this command, restart your computer.

This just moves the serves file for the desktop notifications. So if you want to get the notifications back, you can do so with this command (and a restart):

sudo mv /usr/share/dbus-1/services/org.freedesktop.Notifications.service.disabled /usr/share/dbus-1/services/org.freedesktop.Notifications.service