One thing most help desk organizations do NOT do in calculating cost per call is, include the support cost beyond the help desk (i.e. second and third level support whether captive or outsourced). This leads to misleading and even detrimental management information.
In the extreme, the lowest cost per call would be seen in the help desk that dispatched out the most of their service incidents the quickest, thus saving greatly on their own labour and phone costs while driving total costs up as the inefficiencies from buck-passing creep in. Any cost per unit measurement that focuses only on a portion of the whole is worthless without the full picture.