Help me grow this list by recommending free programs that are useful.
Sometimes, the difference between being a toolkit, a visualizer and a molecular editor (atomistic modeling) is small, because many toolkits and visualizers can also do some function of atomistic editing. So only the categories of Toolkits and Visualizers are defined.
For the QM codes, see DFT Basis Sets & Programs, for large-scale molecular design, see the page Materials Modeling Suites or the Molecular Dynamics and QM-MM Programs.
VASPKIT
http://vaspkit.sourceforge.net/
Alloy Theoretic Automated Toolkit (ATAT)
http://brown.edu/Departments/Engineering/Labs/avdw//atat/
Atomic Simulation Environment (ASE)
https://wiki.fysik.dtu.dk/ase/
ChemShell
OpenMM
Mdtraj
https://mdtraj.org/1.9.4/index.html
AmberTools20
https://ambermd.org/AmberTools.php
MDAnalysis
https://docs.mdanalysis.org/stable/
LIBRA
https://quantum-dynamics-hub.github.io/libra/tutorials.html
LICHEM
https://github.com/CisnerosResearch/LICHEM
Packmol
http://m3g.iqm.unicamp.br/packmol/home.shtml
PyEMMA
http://www.emma-project.org/latest/
Jupyter Notebook
RStudio
ChemVox
https://www.amazon.com/dp/B08G1C97J5
RDKit
WebMO
MolView
https://github.com/moleview/moleview
stk-vis
https://github.com/lukasturcani/stk-vis/releases/tag/v2020.09.17.0
cgbind
Mercury
https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mercury/
Notes: single crystal x-ray, but can load any structure with correct format (eg PDB)
VESTA
http://jp-minerals.org/vesta/en/
Can visualize and edit/build periodic structures.
Avogadro
Notes: structure visualizer, built-in molecular mechanics (MM) force fields for structure minimization/optimization, periodic/unit cell generation, orbital visualizer and input extensions for QM programs.
ChemCraft
https://www.chemcraftprog.com/
ACD Labs
PyMol
Jmol
Gabedit
http://gabedit.sourceforge.net/
Molekel
https://ugovaretto.github.io/molekel/
RasMol
VMD
https://www.ks.uiuc.edu/Research/vmd/
CHIMERA
https://www.cgl.ucsf.edu/chimera/
IQMol