How can I make a missile home to an enemy in arc fashion? (Unity 4.3 2D)

I suggest, using iTween, where you set your waypoints, the easiest way to define this waypoints instead of using a formula, just add 4, the first, your origin, second and third, at 1 third between origin and destiny but with the y above them depending on how your desired arc is, and the fourth your destiny, itween WILL interpolate the movements, after defining that you could play a little with the type of movement, as linear, cuadratic, spring, etc, the code for i tween is something like this

 public Transform[] waypoints;
 public float m_speed = 1.0f;
 public GameObject player1;
 private int i = 0;
 private bool moving = false;
  
 public void Update() {
 if (!moving && i < waypoints.Length - 1) {
 i++;
 moving = true;
 iTween.MoveTo(player1,iTween.Hash("position",waypoints[i],"speed",m_speed,"easetype","linear", "oncompletetarget",gameObject, "oncomplete", "Done"));
 }
  
 }
  
 public void Done() {
 moving = false;
 }

  

And another solution to add to the mix. Use the Sin() function to calculate a loft for the missile over the distance traveled. Take the script below and attach to a sphere in the scene. Click the mouse to shoot the sphere to that position:

 #pragma strict
  
 var traveling = false;
 
 function Update() {
     if (!traveling && Input.GetMouseButtonDown(0)) {
         var pos = Input.mousePosition;
         pos.z = 10.0;
         pos = Camera.main.ScreenToWorldPoint(pos);
         ArcToTarget(pos, 0.35, 1.0);
     }
  } 
  
 function ArcToTarget(targetPos : Vector3, arcFraction : float, time : float) {
     traveling = true;
     var startPos = transform.position;
     var timer = 0.0;
     var arcDist = (targetPos - startPos).magnitude * arcFraction;
     
     while (timer < time) {
         var pos = Vector3.Lerp(startPos, targetPos, timer / time);
         pos.y += Mathf.Sin(Mathf.PI * timer / time) * arcDist;
         transform.position =  pos;
         timer += Time.deltaTime;
         yield;
     }
     transform.position = targetPos;
     traveling = false;
 }

Let's assume we have 3 points: A (start), B (middle) and C (end). We linearly interpolate over time between A and B, as well as B and C. Meanwhile, we interpolate between the result of the two. The code presented below should work perfectly. Simply call QuadraticCurve in the Update() method. Subsequently, increment the time as we want to go from 0 to 1: time += Time.deltaTime;

 private Vector3 LinearInterpolate(Vector3 start, Vector3 end, float time)
 {
     return start + (end - start) * time;
 }
 
 private Vector3 QuadraticCurve(Vector3 start, Vector3 middle, Vector3 end, float time)
 {
     Vector3 line1 = LinearInterpolate(start, middle, time);
     Vector3 line2 = LinearInterpolate(middle, end, time);
     return LinearInterpolate(line1, line2, time);
 }
 private void Update()
 {
     transform.position = QuadraticCurve(startPoint, middlePoint, endPoint, 
     duration);
     durtation += Time.deltaTime;
 }