There's an octave-zenity package which among other things, supports notifications.
Originally Posted by LukeMasters
It's part of the Ubuntu repositories.
zenity_notification (text, icon)
If you download the development version with SVN, it's much more complete. Other than a one-time notifications, the function you can create a icon on the toolbar and use standard error, info, question and warning icons. The whola package allows to create many dialog boxes such as file selection, error messages, list of options with radio buttons or check boxes.