Matthew Perry poses the question: Why is the command line a dying art?. Funny how these things go--I was thinking about posting on this same topic just the other day, although I may be repeating myself.
The efficiencies of the command line cannot be overstated. I too have seen that deer in the headlights look when a GUI-only user is first exposed to a command prompt. I have also seen people spend days on a data conversion project that could easily be accomplished in hours (or less). Once we get over the initial reaction of "Oh no! I have to learn something new", most people find the command line a powerful tool.
For example, here is a simple shell script to convert shapefiles in a directory from their current (in this case projected) coordinate system to WGS 84:
#!/bin/sh for shp in *.shp; do ogr2ogr -t_srs EPSG:4326 wgs84_shapes $shp done
This simply takes every shapefile in the current directory and converts it to WGS 84 and places it in the wgs84_shapes subdirectory. If you don't know what an EPSG:4326 is or need help with projections and coordinate systems, check out the Spatial Reference website.
Total runtime for converting 91 shapefiles was about 47 seconds--way faster than you could do it pointing and clicking.
If you are a Linux or a Mac user, you can take that little shell script and use it directly. If you are a Windows user, you can use the batch language to write a similar script, or better yet install MSYS or Cygwin. With MSYS or Cygwin you can run the script above as-is on Windows.
Don't get me wrong--using a GUI is great, however when you have huge quantities of data to convert there is no better way than the command line.