Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
SnapGene Viewer - SnapGene offers the fastest and easiest way to plan, visualize, and document DNA cloning and PCR. You can easily annotate features and design primers.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
UGENE - UGENE is free open-source cross-platform bioinformatics software
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
DNADynamo - DNA analysis, cloning and sequencing software