Visualization

Mercury Pic Mercury (Freeware) (Win)
Mercury is a very nice visualization program provided by the Cabmridge Crystallographic Database. It is very good at reading files with multiple sets of coordinates. It is not good for biomolecules however, although it can read PDB files. The graphics that it generates are good but not the best. However some of its tools are unique and useful. It is a must have.
3 Molmol (Freeware) (WIN)(UNIX)(OSX?)
This is one of the classic programs for the visualization of biomolecules. It is mostly specific for NMR structures but can be used for any PDB. A bit hard to get used to but very powerfull.
DS Viewer WS Viewer Pro Trial (30 Day Trial, registration)(Win)
There used to be a lite version of this software that was free but apparently it is not available anymore. I do list it here though because it is a very powerful suite of programs that provides excellent Visualization for Biomolecules and small molecules alike.

VMD (Visual Molecular Dynamics) (Registration)(Win) (UNIX) (OSX)
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.