ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
Epic Pen - A windows tool for drawing over your desktop and applications
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
gInk - An on-screen on-screen annotation software for Windows.
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
Gromit-MPX - Create annotations by directly drawing on your screen.