OpenAstexViewer is an LGPL-licensed 3D molecular visualization tool written in Java. With the obfuscated jarfile weighing in at 1 MB, OpenAstexViewer could make a good choice for use in Web applications.
There are now at least two open source, feature-rich 3D molecular visualization tools written in Java (the other being Jmol). Are there any others?
Credit: thanks to Noel O'Boyle for spotting this.