Open program icons would reside in the System Tray by the Clock and program shortcut icons would reside in the Quick Launch by the Start button. Using this approach, there would be an Expand/Collapse button next to the Start button and another next to the Clock on the Taskbar.
It would be easy to differentiate program shortcut icons from open program icons if Microsoft employs the same approach that they took in the Quick Launch and System Tray portions of the Taskbar in XP & Vista.