Epic Pen - A windows tool for drawing over your desktop and applications
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
gInk - An on-screen on-screen annotation software for Windows.
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
Gromit-MPX - Create annotations by directly drawing on your screen.
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.