CanvasMol allows you to model molecules right in your browser using the HTML5 Canvas element and javascript.

Processing.js is "an open programming language for people who want to program images, animation, and interactions for the web without using Flash or Java applets. Processing.js uses Javascript to draw shapes and manipulate images on the HTML5 Canvas element. The code is light-weight, simple to learn and makes an ideal tool for visualizing data, creating user-interfaces and developing web-based games."

Great stuff. I've used Processing (in its java incarnation) for a number of years for various visualization tasks. Processing.js is looking spiffy, too.