AUDENS
It says: AUDENS is a tool for automated de novo sequencing of peptides. It has a flexible preprocessing module which is designed to distinguish between signal and noise peaks.
License: Freeware, but based on Java
http://www.ti.inf.ethz.ch/pw/software/audens/
Gromacs
It says: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles..
License: Freeware, source code available
ImageJ
You can perform densitometric analysis (analysing western blots) if you follow this method.
License: Freeware, but based on Java
ImageLab
Software for 1-D data analysis, for quantification of Western and Southern blots.
License: Commercial, can be downloaded free after registration and used in basic mode
http://www.bio-rad.com/de-de/product/image-lab-software
Image Studio Lite
It says: Free Western Blot Analysis Software.
License: Free, but registration required for download
http://www.licor.com/bio/products/software/image_studio_lite/index.html
iMol
It says: iMol is a free molecular visualization application for Mac OS X operating system.
License: Freeware, but last update was 2007
http://www.pirx.com/iMol/index.shtml
LabImage
It says: The LabImage Software Platform provides a unique approach for all bio-imaging needs from image analysis up to automation and device controlling. LabImage provides the world only Imaging Application Pool.
License: Commercial, free Trial
http://www.kapelan-bioimaging.com
Protein-ms
It says: Tools for mass spectrometry, especially for protein mass spectrometry and proteomics.
License: Freeware, Source code available.
http://sourceforge.net/projects/protms/
PyMOL
It says: PyMOL is a user-sponsored molecular visualization system on an open-source foundation.
License: Only old versions are free for academic use, new versions for paid subscribers only
Swiss-PdbViewer
It says: Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time.
License: Freeware
UCSF Chimera
It says: UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
License: Freeware
https://www.cgl.ucsf.edu/chimera/
VMD
It says: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
License: Freeware
http://www.ks.uiuc.edu/Research/vmd/