About ten years ago, in the boom years of 3D geodata visualization, expensive expert systems appeared. Systems as the costly LandeXplorer, developed by 3DGeo in Potsdam, later acquired by Autocad, were developed to visualize the z-dimension of geodata. Proprietary Arc Scene could be used, though Arc Scene was not as powerful as LandXplorer, but quite OK, unlikely users needed a license from ESRI.
Open source alternatives
Only a few open source alternatives existed. Paraview should be mentioned . Paraview, which I used to map soil contamination, improved a lot and nowadays it´s worth a look. Nviz, a GRASS GIS module for 3D could be used and Fledermaus, a system for the 4-dimensional rendering of geodata were alternatives.
All in all visualizing the third dimension was not affordable or a pain in the ass (sorry for the hard words).
A plugin for QGIS was developed, to use three.js within QGIS: http://qgis2threejs.readthedocs.io/
QGIS2three.js provides a powerful, extremely versatile tool for a visualization of z-dimensional data within web browsers.
Even quadtrees can be built for data compression purposes. So the plugin gives the user a powerful open source tool, for developing all kind of 3D (geo-)data visualization usable within web browsers.
If you plan to do some 3D mapping of geodata for the web, my recommendation is, take a look on QGIS2Three.js.