This demo shows one way to deploy an interactive applet like Jmol on clients lacking the Java plugin.
The technique is based on Websockets, a bi-directional communication protocol that runs over TCP. Currently, Websockets are supported natively on the most recent versions of most standards-compliant browsers. Websockets are also supported on Internet Explorer and other legacy browsers using a Flash implementation.
I recently wrote about WebGL and its application to chemistry, especially in the area of 3D visualization. One problem with WebGL is that it may or may not ever make it to Internet Explorer, which is widely-used in pharma.