JChemPaint
ChemDraw
ACD/ChemSketch
ChemDoodle
Avogadro
BKchem
MolView
MedChem Designer
Gnome Chemistry Utils
ChemDraw
Avogadro
ACD/ChemSketch
ChemDoodle
BKchem
Ptable
Periodic-table.io
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I'd recommend using "JChemPaint" which is a 2D editor. It also contains lots of templates, or you can just go to a site such as pubchem to copy the SMILES representation of a molecule and then have JChempaint draw the structure by just pasting the string. Source: 12 months ago
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
ChemDoodle - Chemical drawing and publishing software for desktop, web and mobile. Affordable and used by thousands of scientists around the world. Free trial available for immediate download.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
MolView - Open Source online service