I TA for a 3D Visualization course, and in my opinion there is certainly a place for 3D visualization in GIS.
For example, bringing a DEM (Digital Elevation Model) in ArcScene (or an equivalent program) allows you to view the X, Y AND Z (elevation) values. You can then bring in additional layers that have no elevation reference and "steal" the DEM's Z-values. These layers would essentially be draped on top of the DEM. From here, you can do all sorts of neat things, like create a viewshed for a particular point (e.g., mountain top), create custom animations (e.g., fly-throughs), or simulate certain scenarios (e.g., flooding a given region).
Additionally, Google has an excellent 3D Warehouse which contains thousands of customized symbols that have been digitized by people across the world using Google Sketchup. Although many of these symbols may not be worth a second look, there are also some extremely detailed models that can be found and downloaded (a star rating helps identify these). Once downloaded, these images (common extension .skp) can be used as the symbology for a simple point feature found in ArcScene. Adding an offset to this point shapefile then allows your new image (e.g., a black hawk helicopter) to appear to be flying on top of your landscape.
Here are a few snapshots of these examples:
Initally, this is what the terrain looks like:
This is what the terrain looks like after a 10m rise in water levels:
And this is what the terrain would look like after a 30m rise in water levels:
Again, this is just a visual representation of the data and should certainly be taken with a grain of salt. What is the resolution of the DEM that was used? How accurate is the data? Etc. These are questions that need to be addressed before being able to take anything away from this on an analytic point of view.
Still, when it comes down to it, it's important to be able to view your data in different ways, and 3D Vis provides a whole new way to view data that 2D platforms simply can't provide. After all, we live in a 3D world, and being able to capture this added dimension when viewing your map can really help to put things in perspective.