One can think of the windows in a GUI as a series of planes parallel to the surface of the monitor.
This confers a speed advantage to the user as the computer does not need to render unseen objects.
In early real-time 3D graphics, Z-order was applied on a per-polygon basis to avoid using Z-buffer, which was considered expensive at the time.
In modern 3D graphics, Z-order is used for order-dependent rendering, for example with semi-transparent objects.
In particular the CSS property that sets the stack order of specific elements is known as the z-index.