Ubuntu has desktop notifications at the bottom of the screen. My question is how to use it with Java. I couldn't find a solution for this. I use Gnome-shell, but does it work on the same way with Unity? And has Debian also the same notification system? And if you know the answer, I hope you will give an example so I'll understand it better.
The SystemTray and TrayIcon should do what you need. If not, maybe Twinkle will:
Twinkle lets you create desktop notifications from your Java Swing application with ease!