Ubuntu's ambient notification system, styled after the Mac Growl interface and first arriving in April's 9.04 release, can be very helpful. They can also be very annoying when they block application closing. This config editing work-around moves them elsewhere
An Ubuntu Forums user details a few steps that move Ubuntu's notifications from the upper right corner of your desktop to the lower left. The top right corner seems like the best place to stash notifications, until you realise that they block the mouse from clicking on any controls or windows underneath that shaded little pop-up, which then stays around even longer when you hover your cursor over it.
The fix requires downloading and installing the source code for the notifications, and might require dealing with additional dependency installations if you get back errors on trying to install the source code. After it's done, however, your notifications now appear in the lower left, and they're less intrusive on your desktop experience.