Some links to the pages I thing are worth to see.
http://zinc.icho.edu.pl The webpage of Grelas group. Take a look, what they are doing.
http://bkchem.zirael.org The BKchem homepage. BKchem is a free drawing program, for sketching chemical molecules. It is written in python and works also in modern operating system including windows, linux and BSD family systems. It can export drawings to eps, ps, pdf openoffice and svg formats. Really worth using.