yes they do
teamspeak for example is in the alt+tab list and in the tray (not in the taskbar)
!TasksMinimize has no effect on it
!ShowDesk has no effect on it too (i loaded the showdesk module)
!MinimizeWindows effects it but it bugs the windows...

id just like to have a function to minimize all foreground windows correctly
there was a very simple vbs script for that which sadly only works with the windows shell