Mark the beginning area of all popup windows.

GUI.Window behaves somewhat differently in the editor than inside your games. In games, GUI.Window pops up a window on your screen. In the editor, GUI.Window shows a subwindow inside one of your editor windows. Begin/EndWindows is used to determine where these can go. You need to have all calls to GUI.Window or GUILayout.Window inside a BeginWindows / EndWindows pair. Like this:

Simple editor Window with a window and a button inside.

	class GUIWindowDemo extends EditorWindow {
		// The position of the window
		var windowRect = Rect (100,100,200,200);
		// Main GUI Function
		function OnGUI () {
			// Begin Window
			BeginWindows ();
			
			// All GUI.Window or GUILayout.Window must come inside here
			windowRect = GUILayout.Window (1, windowRect, DoWindow, "Hi There");		
			
			// Collect all the windows between the two.
			EndWindows ();			
		}
		
		// The window function. This works just like ingame GUI.Window
		function DoWindow () {
			GUILayout.Button ("Hi");
			GUI.DragWindow ();		
		}
		
		// Add menu item to show this demo.
		@MenuItem ("Test/GUIWindow Demo")
		static function Init () {
			EditorWindow.GetWindow (GUIWindowDemo);
		}
	}

The placement of the BeginWindows / EndWindows pair determines where popup windows will appear; all windows are clipped to the clipping area defined by GUI.BeginGroup or GUI.BeginScrollView. A small example of that

Simple editor window with a window and a button inside using scroll bars.

	class GUIWindowDemo2 extends EditorWindow {
		// The position of the window
		var windowRect = Rect (100,100,200,200);
		// Scroll position
		var scrollPos = Vector2.zero;
		function OnGUI () {
			// Set up a scroll view
			scrollPos = GUI.BeginScrollView (
				new Rect (0, 0, position.width, position.height), 
				scrollPos, 
				new Rect (0, 0, 1000, 1000)
			);
			// Same code as before - make a window. Only now, it's INSIDE the scrollview
			BeginWindows ();	
			windowRect = GUILayout.Window (1, windowRect, DoWindow, "Hi There");				
			EndWindows ();
			
			// Close the scroll view
			GUI.EndScrollView ();
		}
		
		function DoWindow () {
			GUILayout.Button ("Hi");
			GUI.DragWindow ();		
		}
		@MenuItem ("Test/GUIWindow Demo 2")
		static function Init () {
			EditorWindow.GetWindow (GUIWindowDemo2);
		}
	}