formerly University of Missouri-Rolla
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