1. A system for comprehensive treatment planning, evaluation and measurement of quality of care of an orthodontic patient comprising: a workstation having a computing platform comprising a graphical user interface, a processor and a computer storage medium; and a set of one or more reference databases accessible to said workstation; wherein said computer storage medium contains digitized records pertaining to a patient, said digitized records including image data, text data, and a three-dimensional virtual model of said patient wherein said virtual model includes a three dimensional dentition model of said patient; wherein said computer storage further contains a set of interactive software instructions enabling an user in planning and evaluating orthodontic treatment of said patient; wherein said computer storage further includes software instructions providing graphical user interface tools for providing said user with access to said digitized records for planning and evaluating orthodontic treatment of said patient; wherein said interactive software instructions allow said user to simulate various possible treatments for said patient on the workstation and visualize the results of proposed treatments on the user interface in order to arrive at a target treatment for said patient; wherein said set of software instructions include instructions for evaluating at least one of the following criteria pertaining to orthodontic treatment: a) treatment efficiency criterion; b) treatment effectiveness criterion; c) patient connectedness to treatment criterion; d) treatment timeliness criterion; e) treatment safety criterion; and f) treatment equitability criterion; wherein said computer storage further includes software instructions for designing shape and configuration of customized orthodontic appliances based upon said target treatment for said patient.