Swiss Protein Databank is best at modeling proteins (and performing a myriad of calculations).

Download SwissPDB (777kB)

SwissPDB Tutorial

ArgusLab

ArgusLab allows the user to create and/or view small molecules as well as proteins.  Powerful computational abilitites also.  Requires a short registration (no denials I've heard of), and requests that the following citation be used: 

ArgusLab 4.0.1
Mark A. Thompson
Planaria Software LLC, Seattle, WA
http://www.arguslab.com

Download ArgusLab

ArgusLab Tutorial

Pov-Ray

Pov-Ray is a general rendering program that we will use to create a final image of our molecule.

Download Pov-Ray      (10MB)

Pov-Ray Tutorial

I recommend the 32bit version if you run Windows