US governmental molecular modelling resource.
http://cmm.info.nih.gov/modeling/

http://www.ncbi.nlm.nih.gov

http://www.nsf.gov

The National Science Foundation

Francesco Bennardo:members.xoom.it/geomol/
After you download Chime, you are able to see the molecules. Please note that the Chime is free, but even without the plug-in, you can see the great big ray-tracing pictures, the HyperChemTM section and the MathematicaTM section.
"This site is dedicated to: Linus Carl Pauling (1901-1994), Chemistry Nobel Prize 1954, Peace Nobel Prize 1962
Peter Mitchell (1920-1992), Chemistry Nobel Prize 1978
Scipione Valentini (1915-1979), Ispettore Scolastico, Politico e Intellettuale"

The Interactive Library
edinformatics.com/il/il.htm

Akira Dobashi at Tokyo University of Pharmacy and Life Science, Department of Structural Organic Chemistry. Presently research work is focused on the molecular modeling of pharmaceutical structures through computational chemistry, and the recognition of molecular chirality and shape. This site gets 5,000+ hits/day.http://triton.ps.toyaku.ac.jp/~dobashi/english/index.html

Chem Symphony:
http://www.chemsymphony.com/index2.htm
Java based molecular visualization.
"NetGenics creates flexible solutions that allow pharmaceutical and agriscience companies to accelerate product development in the development of new drugs, gene therapies and agricultural products while decreasing their research costs." The main NetGenics web-site.
http://www.netgenics.com/index.htm

One could conceivably use general 3D modelling and rendering applications for the creation and visualization of molecules. Dedicated molecular modelling applications are superior in their ease of use and exactitude in details such as bond distances and angles as well as atomic radii. An accurate representation of macromolecules just isn't possible without the multitude of atomic coordinates contained in a PDB file. Perhaps one day when Hal 9000 computers become household items, even the general 3D applications will be able to use files such as the PDB files. Until then it must be pointed out that in this regard approximation has its value. Aesthetically pleasing animations made with an emphasis on general principles and mechanisms in place of strict adherence to detail can be created with general 3D modelling and rendering applications.

Dedication to Dr. Marjorie Caserio.