A colleague has just pointed me to ChemPad, an interesting piece of software that allows chemists to draw chemical diagrams directly into a computer on a Tablet PC. It was designed as a tool to enable undergraduate chemists to quickly enter chemical structures and generate 3D diagrams with which they could gain a deeper understanding of structures. Hash and wedge bonds are understood and are converted faithfully to 3D, for example.
From the point of view of teaching chemistry undergraduates, such software may be preferable to ChemDraw and friends as it allows them to develop the skill of drawing diagrams by hand. Of course, not everyone has a tablet PC but one could imagine similar software for the iPhone or just a regular PC driven by a mouse.
ChemPad is free but not open source, and Windows only. The ChemPad website has tutorials and videos of the software in use.