Is it possible to script rutines in QGIS (python) and then runing them remotely? To illustrate, can I through a shell (ssh or telnet) ask to QGIS to transform a shapefile into a gjson format? Mostly, I'm thinking in the interaction of QGIS with another software like R for example, where I can generate command lines. (I'm not talking about QGIS internal command shell)
Most of the tools inside the qgis GUI are actually calls to gdal executables or python scripts, so the answer is yes.
You would ssh into your shell, and type for example: /path/to/gdal/gdal_translate parameters