See also the following posts for ISISDraw, MarvinSketch and BKChem.
Chemtool
I didn't get along with this at all. I managed to import a few structures from the templates, but e.g. the clean molecule function didn't actually work, although it's there. Selecting, deleting etc. were all a bit non-intuitive (to me -- this is obviously very subjective)
Easychem
I can't find any templates. Drawing becomes a bit tedious since I didn't find an easy way of converting an existing bond from e.g. single to double.
gChemPaint
It's pretty straightforward to use and I like it the best of the three. However, it's still very sparse even compared to e.g. bkchem. It certainly works if you quickly need to make a simple structure. There's no clean function.
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