Notify OSD has been in Ubuntu for a long time yet for some odd reason, it never supported any kind of customizations so if you wanted to change it's color or position you had to compile it with the new settings. But there is an Ubuntu PPA with a patched Notify OSD for Ubuntu 9.10 Karmic Koala and Ubuntu 10.04 Lucid Lynx which supports customizations via a simple text file so you don't have to compile it and can change the Notify OSD settings on the fly.