I am a professor at the University of Wisconsin Oshkosh. I use Jmol for Web displays to help students visualize molecular shapes and orbitals as well as in class assignments where students develop web pages with Jmol molecules in them.
1) the Export_to_Web tool inside Jmol which automates the process of making simple web pages containing Jmol and some basic controls.
2) the surfaceTool, which so far provides a GUI for controlling slicing of surfaces. Eventually it should allow full control of surface display including color, transparency and mesh.
3) Jmol in SageMath
More information is available at my web site.