Atom World (Popularity: )
http://www.jlc.net/~aretee/atomworld/ Beautiful space-filling atomic models showing simultaneous polar and covalent bonding. Make any molecule from diamond to DNA; you'll understand chemistry like never before.
Chemist's Art Gallery (Popularity: )
http://www.csc.fi/chem/gallery.phtml Visualization is a key to understanding how molecules behave and react, and in designing chemicals for particular purposes. The Chemist's Art Gallery contains visualizations and animations in chemistry done at ...