In your Ubuntu machine, when you click on the ‘X’ (close button) on any applications, you will find that some of them will exit while some will minimize to the system tray. Unless you know the capability of the particular application, you will have to guess every time you click on the X button whether it will close or minimize. For example, in Ubuntu Hardy, I can click the X button on Transmission and it will minimize to the system tray, but in Intrepid, it will exit when I click the X button. It is kinda confusing and troublesome since what I really want to do is for it to minimize to the tray and download the torrent in the background.
For those who want to eliminate all the guess work or want to save desktop space by minimizing all the unused applications to the system tray, AllTray is the application to do it.