How to sort Windows by z-index?

You cannot get a Window's Z Order information from WPF so you must resort to Win32.

Something like this ought to do the trick:

var topToBottom = SortWindowsTopToBottom(Application.Current.Windows.OfType<Window>());
...

public IEnumerable<Window> SortWindowsTopToBottom(IEnumerable<Window> unsorted)
{
  var byHandle = unsorted.ToDictionary(win =>
    ((HwndSource)PresentationSource.FromVisual(win)).Handle);

  for(IntPtr hWnd = GetTopWindow(IntPtr.Zero); hWnd!=IntPtr.Zero; hWnd = GetWindow(hWnd, GW_HWNDNEXT)
    if(byHandle.ContainsKey(hWnd))
      yield return byHandle[hWnd];
}

const uint GW_HWNDNEXT = 2;
[DllImport("User32")] static extern IntPtr GetTopWindow(IntPtr hWnd);
[DllImport("User32")] static extern IntPtr GetWindow(IntPtr hWnd, uint wCmd);

The way this works is:

1. It uses a dictionary to index the given windows by window handle, using the fact that in the Windows implementation of WPF, Window's PresentationSource is always HwndSource.
2. It uses Win32 to scan all unparented windows top to bottom to find the proper order.