Answer by Ent

Hi, been reading through some other postings and gathered some interesting things together that may help some other people reading this and needing a more complex solution for different reasons and using a window below the GUI.

// Boolean for when mouse is over window

var onMouseOverMenu : boolean = true;

// Creation point of window

var windowRect : Rect = Rect (20, 20, 200, 300);

// Rect of window. Can also be windowRect if the creation point is not needed anymore
// after the creation of the window

var windowRectBox : Rect;

function Update(){

//if you have multiple GUIs you could use something like:
// //Dont forget to change onMouseOverMenu to a boolean Array and to refer to this script.
// var isOnMouseOverMenu : boolean = false;
// for (var oMOMPtr : int in onMouseOverMenu)
//    if(onMouseOverMenu[oMOMPtr]==true)isOnMouseOverMenu = true;
// if(isOnMouseOverMenu){
// //... enter script here
// }

if (onMouseOverMenu) {
    // ... enter script here
}   

if (!onMouseOverMenu) {
    // ... enter script here
}   

}

function OnGUI () { windowRectBox = GUI.Window (0, windowRect, WindowFunction, "My Window"); }

function WindowFunction (windowID : int) { // Draw any Controls inside the window here

// Sets a Rect to the size of this window.
var curBox : Rect = Rect(0,0,windowRectBox.width,windowRectBox.height);

// Checks if the mouse is inside of this Rect.
// Due to a Window setting the Event.current.mousePosition to the position refering
//to this window, our Rect starts at 0,0 and not at the creation point of this window.
// Using Input.mousePosition is also a problem due to the creation of a GUI Element being
// refered to from a corner point of the screen (default top left), even if created with
// a Rect and that a Rect or Input always starts from the bottom left corner.
// So if using xyzRect.contains(Input.mousePosition){} and creating a window at xyzRect,
// you will notice that that the xyzRect.contains is not the same position as the window
// created in xyzRect, even thou these are the same Objects. For this to work,
// you would have to create all GUI elements from the bottom left corner.
if(curBox.Contains(Event.current.mousePosition)){
    Debug.Log("Mouse in Menu at " + Event.current.mousePosition);
    onMouseOverMenu = true;
} else if (onMouseOverMenu == true) {
    onMouseOverMenu = false;
}

// ... enter GUI here

}

e.g. if you have an onScreenDisplay wanting to show the distance to an object inside this screen: // place in Update()

//Where the mouse clicks
var ray = Camera.main.ScreenPointToRay (Input.mousePosition);

if (onMouseOverMenu) {
    // ... enter script here
    // ... only cast on gameObjects behind this window (or Rect)

        //Do a raycast from camera in direction of ray,
        //with a distance 100.0 and return hit.
    if (Physics.Raycast (ray, hit, 100.0)) {
        //hit.distance is the distance to the first collider.
        distanceToGround = hit.distance;
        //This draws a line, that shows the ray, in the editor.
        Debug.DrawLine (ray.origin, hit.point);
    }   
}