Unique id numbers for GUI.Window

I'm not sure I understand your question right.

How about just using a list of ints? If you want to generate a new ID, check if the list contains that one, and if yes, generate another one.

The easiest way is to use a "windowID manager" like this:

 // C#
 public static class WindowIdManager
 {
     private static int m_NextId = 2222; // I just start a bit higher to keep space for hardcoded window ids.
     public static int GetWindowId()
     {
         return m_NextId++;
     }
 }

In all your scripts where you need a window ID you just declare a member variable for each window you need like this:

 // C#
 public class SomeScript : MonoBehaviour
 {
     private int m_WindowId1 = WindowIdManager.GetWindowId();
     private int m_WindowId2 = WindowIdManager.GetWindowId();
 }

GUIUtility.GetControlID(FocusType.Passive)

Rect WindowRect = GUI.Window(GUIUtility.GetControlID(FocusType.Passive), WindowRect, Window, " ");