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.
BioEdit - Biological sequence alignment editor
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
Geneious - Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary...