Software

• ChemOffice Professional
  Commercial software for drawing molecular structures, 3D models and many more. High price but most higher education institutes will provide students/staff with free institutional licenses. The molecular sketcher now has a free online version (built using HTML$5$ and JS): ChemDraw online
• MarvinSketch
  Freeware (closed-source) for drawing molecular structures with a wide feature set. In addition to just being able to draw Lewis structures, the software includes plugins to name what you have drawn (systematic/traditional), predict properties, change atom and bond properties, generate stereoisomers, and much more. It is Java based so works on Mac, Windows, Linux and is even available on the web.
• ChemDoodle
  Commercial software for 2D and 3D molecular structures and diagrams and much more. Also has versions for tablet/mobile. An online free version of ChemDoodle is here: ChemDoodle Web Components
• ACD/ChemSketch
  Commercial software for Windows only. Includes a free version with fewer features.
• chemfig
  Free $\mathrm\LaTeX$ package distributed under the LATEX Project Public License 1.3c for creating 2D chemical structures with seamless integration into any type of a document, from a standalone illustration to a textbook or a poster. Since TikZ is used for graphics generation, the functionality of chemfig can be greatly extended. PDF output can also be rasterized by using external tools such as ImageMagick.
• Avogadro
  Free, open source software for generating 3D models and computational chemistry.
• GAMESS
  Free ab initio molecular quantum chemistry program.
• Open Babel: The Open Source Chemistry Toolbox
  Free "Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas."
• RDKit: Open-Source Cheminformatics Software
• Odyssey by Wavefunction
  Commercial software designed to be used for teaching and learning chemistry. Includes high quality molecular simulations of many materials, in-built virtual labs. Excellent animations of many physical and chemical processes.