Hey - yep, you want to use Physics2D.Raycast, not Physics.Raycast. As of 4.3, there are different raycasting systems for the two types of physics engines. To detect clicking on something, I use this:
Vector3 mouseWorldPosition = Camera.main.ScreenToWorldPoint(Input.mousePosition);
RaycastHit2D rayCastResult = Physics2D.Raycast(mouseWorldPosition, new Vector3(0, 0, 0), 0.0f);
if(rayCastResult.rigidbody)
{
// Do Stuff
}