Biomer: online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm images
Chemland: educational java applets (about 40) explaining many principles in chemistry
: any structure you draw is converted to 3D and the Raman and IR spectrum is calculated. The vibrational modes are visualized in VRML.
CORINA: online 3D structure generator from SMILES strings
CyberMol: online 3D structure generator from SMILES strings