1) For a full 3D GIS, the better is GRASS GIS, look at Screenshots of 3D data management or From drone-aerial pictures to DEM and ORTHOPHOTO: the case of Caldonazzo's castle, from example.
Some examples (interactive: you can scale, rotate the representation and many other things) :
DEM with 3D points:
Draped raster on the DEM
Draped geological map with 3D surfaces (2 thrust faults, blue, grey), 3D tubes (boreholes, blue), 3D lines (blue) and 3D points
2) You can also use QGIS and the Qgis2threejs plugin (interactive: you can scale and rotate the representation):
Draped raster on a DEM, with draped 2D polylines (black, red)
3) and you can also use Paraview (from GRASS GIS) , R and even, SketchUp (and Google Earth) or Blender (Visualising QGIS data with Blender, for example) -all the solutions are interactive.