This page emphasizes programs available for Windows, because that is where I have experience. Programs for other platforms and multi-platform programs are included when I have information; I welcome contributions.
All resources posted here are free; some may require that you register in order to download their files.
ChemFormula, a macro for Microsoft Word to help you format chemical expressions. My Download page includes a figure showing what it does, and links to the files. (Written by a student friend of mine.)
ChemSketch and Symyx Draw are programs that allow you to draw organic chemical structures. The drawings can be used as (2D) structures, for example in word processing files, or they can be converted to 3D models. I have posted introductory guides for these free programs; the guides tell you how to get the programs, and then help you get started using them.
Introductory guides: ChemSketch   Symyx Draw
Symyx Draw is a successor to ISIS/Draw. ISIS/Draw itself is no longer available; I will leave the ISIS/Draw Guide, since many have this program. ISIS/Draw - An Introductory Guide.
RasMol is a classic program for viewing 3D molecular structures. You can also perform a variety of manipulations on them. Using RasMol is something like using a box of models, but lets you view much larger molecules. Thousands of "pdb" files are available, for small molecules and for macromolecules, for RasMol. (Some of the newer programs for viewing molecular structures use code or ideas from RasMol.) I have posted an introductory guide for this free program. It tells you how to get RasMol, introduces you to using it, and provides some sources of structures that you can view. It explains how to make your own 3D structure files, using the drawing programs listed above. It also contains some suggestions keyed to my X402 course, Introduction to Organic and Biochemistry.
My Introductory guide for RasMol.
iMol is a molecular viewing program for the Macintosh (OS X). It uses standard source files, such as pdb files. iMol is written with the Mac in mind, and may have superior graphics. http://www.pirx.com/iMol/. I have no personal experience with Mac programs, but will list occasional items referred to me by trusted sources. Thanks to Thien in Massachusetts for calling this one to my attention.
Among the other programs listed above, RasMol has a Mac version available. There was a Mac version of ISIS/Draw, but it is no longer available. Those who happen to have it can use my ISIS/Draw guide.
Jmol allows you to view and manipulate molecular structures on web pages.
* Jmol is a Java-based program that allows the web-page author to provide functionality for viewing molecular structures. No special software is needed by the viewer; however, support for Java must be turned on. For a nice introductory tutorial aimed at the person viewing pages with Jmol, see http://www.bluffton.edu/~bergerd/classes/jmol.html. From Dan Berger, at Bluffton Univ.
Chem drawing in Linux. This page reviews several chem drawing programs available for Linux. The original review is from 2004, with some comments through 2008. The page is now archived: http://web.archive.org/web/20090419235916/http://groundstate.ca/chemdraw. Thanks to Greg in England for calling this site to my attention. If anyone knows of something more recent, please let me know.
Linux4Chemistry. The following page is an extensive list of chemistry software for Linux. It includes software for drawing and viewing molecules -- and more. Note that you can select software categories. http://www.linux4chemistry.info/.
Among the other programs listed above... RasMol, an open-source program, has been adapted for many platforms. Check the RasMol home page, or Google on RasMol Linux for information. The ChemSketch folks suggest how that program may run with Linux.
Marvin Sketch is a molecular drawing program that is part of a suite of chemistry programs. It is available for many platforms. When I asked about drawing programs for the Mac in a chemistry forum, Marvin Sketch was one that was recommended. It is freely available at http://www.chemaxon.com/products/marvin/.
Open Babel - The Open Source Chemistry Toolbox. "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." The heart of it is a program to interconvert molecular structure files from one format to another. It is available for many platforms. It is freely available at http://openbabel.org/wiki/Main_Page. Choose "Get Open Babel" to go directly to the software.
Collections of molecular structures
Some of these may also be listed on other pages.
Atlas of Macromolecules. http://www.umass.edu/microbio/chime/pe_beta/pe/atlas/atlas.htm. Proteins and nucleic acids, including more complex structures, such as viral capsids.
Molecular models. http://www.molecularmodels.ca/molecule/molecule_index.html. Dr Dave Woodcock's collection of PDB files for small molecules, at Okanagan University College.
Protein Data Bank: An Information Portal to Biological Macromolecular Structures. http://www.rcsb.org/pdb/home/home.do.