I had never heard the name Ayatana before Mark Shuttleworth mentioned it during the Ubuntu Podcast. Basically, Ayatana is the overall project for improving desktop experience. Part of that is the whole notification system in Ubuntu 9.04. More here

David Barth sent an email to -devel announcing the opening of Ayatana mailing list and IRC channel (#ayatana on freenode) , to discuss what should be done for 9.10. Mark has already kicked off discussions with a mockup of notification bubbles being visually distinct depending on their priority.