Avogadro

Avogadro is an advanced molecular editor to generate interactive 3D models for practically any chemical compound.

It can be used for computational chemistry, molecular modeling, bioinformatics, materials science, and other related areas. It is compatible with GAMESS, Gaussian, Q-Chem, and MOPAC systems.

Avogadro lets you measure between atoms and bonds. You can also manipulate links and atoms individually, rotating the figure automatically and even accessing a library with pre-created models of all chemical compounds.