Chemsketch:  from ACDLabs, free downloads available for their Chemsketch  and the 3-D viewer.
  HTTP://www.acdlabs.com
This is only available for PC-pentium class machines.

Isis/Draw  from MDL  (Molecular Design Limited) is freeware to academic institutions. You may also get an add-in from ACDLabs (see above) for Isis/Draw that will take the Isis structure and convert it into a 3-D image (Windows only).
  HTTP://www.mdli.com
Go to their download center and to the Free Products area to find the correct file.
Both Mac and Windows versions are available.