Software recommendations for overlaying molecular structures I am looking for a program to overlay the structure of small molecules as an aid for my students in comparing the results of optimization geometries using different optimization methods.

At this stage, we are thinking of atomic coodinates and a visual comparison. However, if it can be complemented with a quantitative comparison that would a welcomed extra.

We work with the Windows versions of Gaussian 09 and GaussView 5.
You can use the "compare" command in the Jmol program, either online or as free-standing program. A tutorial on how to use the program for this purpose is here, http://proteopedia.org/wiki/index.php/Superposition_with_jmol. It outputs the root mean square of the pairwise differences (RMSD) as well as the superposed coordinates.