Do-It-Yourself Molecules:
From 2D to

JChemPaint 2 DIY

JChemPaint 3 DIY

Java Molecular Editor

JavaScript Molecular Editor with JSmol DIY
Does not use Java applets

SketchEl DIY

JSDraw
(Chemene)

jsMolEdit 0.2

jsMolEdit 0.3

Doodler
(ChemDoodle Web Components)