Chemlets (chemistry applet animations)

EDinfomatics Interactive Library - Chemistry – Incredible listing of animations

ChemConnections (UC Berkeley) – virtual demos

irYdium Project (Carnegie Mellon University) – virtual labs and demos, rather sophisticated controls with step-by-step how-to documentation.

Reciprocal Net – distributed database on crystalline molecular structures, including rotating visualizations.

UC-Irvine chemlets – quite nice selection with explanatory links about what’s going on in animation