ESRI ArcScene and Qgis Qgis2threejs extension are good solutions, but do not allow to make any measurement or analyze in a vertical (Z) way. 3D modelers (like blender or 3DSMax) or CAD softwares (like Autocad) are difficult to handle for geographers and are not always compatible with geographic information (shapefiles). Do anyone know any alternative?
Did you try Paraview? http://www.paraview.org/
In the past I did something exporting VTK data from GRASS GIS and importing into Paraview.
http://grasswiki.osgeo.org/wiki/GRASS_and_Paraview
I used to use Terrain Tools by Softree for geoprofiles - quite nice and simple:
http://www.softree.com/products/mapping_terraintools3d.aspx
I use Rhino 3d. Rhino is relatively easy to use, and not too expensive. It is fast, you have all kinds of measurements available, you can render beautiful 3d scenes. But importing GIS data may a little bit difficult, as with all CAD systems. You can export GIS geometry data as DXF files, raster as images along with their foot prints. Their are modules for the graphical workflow modeller Grasshopper, that allow for Shape files and projections (based on GDAL).
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