I use models in several ways in my organic class. The most important use, without question, is to prepare visual images for use in lecture and elsewhere. These images are presented using SPARTAN running on an SGI Indy workstation equipped with the Indy Presenter and overhead projector. This allows me to build, manipulate, and modify models during lecture, as well as to present a mixture of still images and animated sequences.
This picture shows how I use models in class to teach students about the conformational preferences of methylcyclohexane. The images on the left are the equatorial and axial conformers of methylcyclohexane, respectively (upper/green = equatorial, lower/red = axial). The "green" portion of the equatorial confomer has the same structure as the anti conformer of butane (I show this in lecture by moving the butane model so that it becomes superimposed upon the methyl cyclohexane model). The "red" portion of the axial isomer has the same structure as the gauche conformer of butane. Since anti butane is more stable than gauche, we can expect equatorial methylcyclohexane to be more stable than the axial conformer.