Si queremos configurar el navegador predeterminado del escritorio, hay una herramienta muy útil llamada xdg-settings.

Las opciones para cambiarlo son:

$ xdg-settings --list
Known properties:
default-url-scheme-handler Default handler for URL scheme
default-web-browser Default web browser

$ xdg-settings get default-web-browser
midori-private.desktop

$ xdg-settings set default-web-browser firefox.desktop

$ xdg-settings get default-web-browser
firefox.desktop

Esto es válido en Fedora, Debian, tanto para XFCE como Gnome. El paquete que provee este ejecutable es xdg-utils, que da esta información :

Name : xdg-utils
Summary : Basic desktop integration functions
URL : http://portland.freedesktop.org/
License : MIT
Description : The xdg-utils package is a set of simple scripts that provide basic
: desktop integration functions for any Free Desktop, such as Linux.
: They are intended to provide a set of defacto standards.
: This means that:
: * Third party software developers can rely on these xdg-utils
: for all of their simple integration needs.
: * Developers of desktop environments can make sure that their
: environments are well supported
: * Distribution vendors can provide custom versions of these utilities
:
: The following scripts are provided at this time:
: * xdg-desktop-icon Install icons to the desktop
: * xdg-desktop-menu Install desktop menu items
: * xdg-email Send mail using the user's preferred e-mail composer
: * xdg-icon-resource Install icon resources
: * xdg-mime Query information about file type handling and
: install descriptions for new file types
: * xdg-open Open a file or URL in the user's preferred application
: * xdg-screensaver Control the screensaver
: * xdg-settings Get various settings from the desktop environment

Ya no perderé el tiempo buscando entre confusos menús gráficos :-)