Comment 1 for bug 347173

AllTray already lets you click the "close" button to send the application to the system tray. If you want to minimize the application to the taskbar, you can do that by clicking the minimize button; to tuck it neatly away in the system tray, you just click the close button.

Doing it for any program (read: any X Window) in Ubuntu is also possible using AllTray in "click mode". I may be missing something here, so I'll leave the bug open so you can clarify what you mean, but it looks to me like what you already want is largely already there. Would that assertion be correct?