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Jmol is an open-source Java viewer for chemical structures in 3D
with features for chemicals, crystals, materials and biomolecules  (http://jmol.org).
It allows you to handle virtual molecular models in the computer, also within web pages.
I have just published a handbook "How to use Jmol to study and present molecular structures", ISBN 978-1-84799-259-8. It's available from Lulu.com.
Information, preview and online shop at http://biomodel.uah.es/anun/manual-jmol/inicio-en.htm

It aims to be at the same time a tutorial for beginners and a handbook for reference and deepening for more skilled users. It may be of profit for instructors, authors of teaching or popularization material, students, researchers and information portal administrators or designers.

Hope you find it useful!