In a previous post I showed how to use PubChem Editor to draw a complicated molecule and import it into Avogadro using the insert SMILES option. Unfortunately, Avogadro does not interpret the chirality information correctly, and chiral structures often have to be fixed.
In the screencast above I show another program, Marvin Sketch, that allows you to draw a structure in 2D and convert it (correctly) to 3D. The coordinates can then be transferred to Avogadro by saving a .mol file.
I also use Marvin to draw 2D structures for the blog. For example
However, Marvin Sketch is much more than a drawing program. The tools menu contains many powerful cheminformatics tools such as pKa prediction, isomer search, etc.
Marvin Sketch can also be download as a stand-alone program free of charge for academics.