Just a note for future generations -- the correct file to edit to change the system default application for a given MIME type is:

   /usr/share/gnome/applications/defaults.list

This took a surprisingly long time to figure out - mainly because of the existence of other similar files such as /usr/share/applications/defaults.list and /etc/gnome/defaults.list.

Also, you can check the default application for a given MIME type using the following command: xdg-mime query default

As an example, the MIME-type for PDF is "application/pdf".