In the GIS world, a 3 Dimensional object has an X, Y and Z coordinates. Z coordinate is used to draw height. 3 Dimensional map gives a better understanding of the object, in GIS 3 Dimensional map might be TIN image, Digital Elevation Model or any GIS layer with elevation values. To plot these GIS layer with Z value or TIN image or DEM data you need a special kind of GIS software. So here are few 3 Dimensional free GIS software that will help you create and visualize your 3 Dimensional data.
QGIS is an open source software and allows GIS user to create, edit and analyze GIS data. It is evolving every year, and different plugins are added by users. QGIS2threejs plugins allows DEM or any other 3 Dimensional data to plot ted on the QGIS environment. This Tutorial shows how to run the QGIS2Threejs plugins.
GRASS GIS software has about 350 modules to render the map. It runs in QGIS by using plugins. GRASS GIS includes NVIZ component which has the capability of displaying 3D or 4D images. It also support the voxel. This Tutorial shows how to visualize 3 dimensional data using GRASS GIS.
Blender is another opens source 3 Dimensional graphics software which is used for creating animation movies, visual effects, art, 3D prints and many more. Some of the 3 Dimensional GIS processing that can be achieved using Blender are building Terrain model, 3D airphoto and more. You can also create shaded relief map on Blender, here is step by step tutorial. QGIS can be used heavily to create a terrain model, here is a video tutorial using QGIS and Blender to create Terrain model. There are numbers of GIS addons for blender, check Addonscollection.
System for Automated Geoscientific Analyses (SAGA GIS) is a GIS software used heavily for editing spatial data, it was primarily created by the Department of Physical Geography, University of Göttingen, Germany. You can create and visualize 3 Dimensional data on SAGA GIS, here is the step by step tutorial.