If all you're wanting to do is detect whether the mouse position is in an area (e.g. circle or rectangle) in the middle of the screen, that's very easy to do. A point-in-circle test looks like this (untested pseudocode):

inside = squaredLength(point - circleCenter) <= square(circleRadius);

And the point-in-rectangle test looks like this (I think Unity may even have a function for this):

inside =
    point.x >= rect.min.x &&
    point.x <= rect.max.x &&
    point.y >= rect.min.y &&
    point.y <= rect.max.y;

I have put Rect.Contains into MouseOrbit.js in order to create a central exclusion zone, but am unsure how to reverse it. At the moment there is no input from outside the rectangle, but i want there to be no input from inside the rectangle. I have so far...

var target : Transform;
var distance = 10.0;
var rect = Rect (200,200, 450, 450);

var xSpeed = 250.0;
var ySpeed = 120.0;

var yMinLimit = -20;
var yMaxLimit = 80;

private var x = 0.0;
private var y = 0.0;

@script AddComponentMenu("Camera-Control/Mouse Orbit")

function Start () {
    var angles = transform.eulerAngles;
    x = angles.y;
    y = angles.x;

    // Make the rigid body not change rotation
    if (rigidbody)
        rigidbody.freezeRotation = true;
}
function LateUpdate () {
     if (rect.Contains(Input.mousePosition))
     if (target && Input.GetMouseButton(0)) {

        x += Input.GetAxis("Mouse X") * xSpeed * 0.02;
        y -= Input.GetAxis("Mouse Y") * ySpeed * 0.02;

        y = ClampAngle(y, yMinLimit, yMaxLimit);

        var rotation = Quaternion.Euler(y, x, 0);
        var position = rotation * Vector3(0.0, 0.0, -distance) + target.position;

        transform.rotation = rotation;
        transform.position = position;
    }
}

static function ClampAngle (angle : float, min : float, max : float) {
    if (angle < -360)
        angle += 360;
    if (angle > 360)
        angle -= 360;
    return Mathf.Clamp (angle, min, max);
}