Visualising the structure of molecules in 3D on the web is useful for education and other communication activities. Web-based java and HTML5 viewers exist that allow this. However, I think that gaming technologies will allow models to be used in more sophisticated learning objects where users can select and highlight specific structural or functional regions of the molecules. This will enhance the learner’s experience and make it more immersive.
I have used WebGL, Flash and Unity3D, all 3D technologies that are popular with online gaming developers, to visualise molecules.