You should cite 3D-ID in accordance with standard professional practice as:
Slice, D. E. and A. Ross. 2009. 3D-ID: geometric morphometric classification of crania for forensic scientists. Version <i>.<j> (<ddmmyyyy>). http://www.3d-id.org
where the elements between '<' and '>' are to be replaced with appropriate information from the Help|About dialog of the version of the program you are using.