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Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. ...

Quick3dApplet - a java applet for displaying interactive 3d on a webpage. This is a fast renderer that should be viewable on most browsers without the viewer having to load extra plugins (uses java 1.1). It can read the 3ds model format.

Java 3D engine. Applet demo is available at the project homepage.

JetSteam-3D is 3D GIS technology developed by Alchemedia. that allows the streaming of image,DEM,X3D,and WFS data to an applet. The javascript enabled applet allows the creation of 3D enabled WebGIS applications using typical AJAX techniques.