+ * Get the z-priority for a given window. This is defined as an arbitrary integer value which is used only in
+ * comparison with other z-priority values; a window with a given z-priority will appear above other windows with
+ * a lower value, and below those with a higher one. (The ordering within z-priorities can be mixed).

'...arbitrary integer value ... used only ...; ' is maybe not so relevant?

Suggestion for the last part: (The ordering of windows with equal z-priorities is arbitrary.) ?

===================

+static inline int GetWindowZPriority(const Window *w)

'inline' does not seem too needed.
If you are worried about performance, a better idea is to store "GetWindowZPriority(this)" below.
(A decent C++ compiler will inline the call and cache the above value by itself already, so it won't make a big difference either way.)

===================

+		case WC_CONSOLE:
+			return 5;
+
+		case WC_DROPDOWN_MENU:
+			return 4;

This hides dropdown-menus behind the console, which means you cannot use a dropdown any more.
Unless you have a good reason for this order, I'd suggest to swap these.

Another window you may want to consider is WC_ERRMSG.

===================

+		default:
+			return 0;
+
+		case WC_MAIN_WINDOW:
+			return -1;

If you add 1 to all numbers, you can make the function return an uint.

===================

+	if (w != NULL) {

Your editing made the if/else statement difficult to read, and it introduced some dead code.
In the 'else' of the above 'if (w != NULL) {', the condition 'if (_z_front_window != NULL) {' never holds, since you just tested that here.

I suggest a rewrite of this code. The general preference is to have a sequence of cases, and deal with one at a time, completely. For example

   ...
   if (A) {
      ...
   } else {
      if (B) {
         ...
      } else {
         ...
      }
   }
}

can also be written as

   ...
   if (A) {
      ...
      return;
   }

   if (B) {
      ...
      return;
   }

   ...
}

which is easier to read as you don't have to navigate through all the if/else branches and remember all test results along the way.


In the function, the 'w == NULL' seems the simpler case, so I'd do that one first, like

	...
	if (w == NULL) {
		/* the 'else' part here. */
		return;
	}

	/* the 'then' part here. */
}

I am sure you can find a nice code layout.

===================

+			assert(!w->z_front || w->z_front->window_class == WC_INVALID || w->window_class == WC_INVALID || 
+				GetWindowZPriority(w->z_front) >= GetWindowZPriority(w));

It took me a while to understand this, but it seems correct.
Three minor code-style issues:
 - "!w->z_front" should be "w->z_front == NULL", as w->z_front is not a boolean value.
 - at the end of the first line is a trailing space character, which should not be there.
 - the second (and all next lines) of a multi-line statement should indent by 2 TAB characters.

The last item is for cases like

if (foo != 0 &&
		foo != 1) {
	foo = 1;

A single indent at the second line would make it look like it belongs to the 'then' part.