ChemDoodle v1.4.0 now contains a function for rotating structures in 3 dimensions. Rotations are performed on a virtual trackball and are very intuitive. As you can see from the animations below, structures can now be portrayed in a very captivating fashion. All file formats will now read and write the z-coordinate. The button for entering the 3D rotation state is displayed as a grasping hand and is located next to the transform tool button as shown in the image below. Expect ChemDoodle v1.4.0 to be released shortly after the holidays.
UPDATE: ChemDoodle v1.4.0 was released on 12/19/08.