How do I reset gnome font configuration?

Ubuntu 16.04 and after

gconftool-2 has been superseeded by gsettings on Ubuntu 16.04+ and in other GNOME based systems.

Nowadays you can simply run the following in a terminal window to reset all your desktop font settings:

gsettings reset org.gnome.desktop.interface font-name
gsettings reset org.gnome.desktop.interface document-font-name
gsettings reset org.gnome.desktop.interface monospace-font-name
gsettings reset org.gnome.desktop.wm.preferences titlebar-font
gsettings reset org.gnome.desktop.interface text-scaling-factor

In versions prior to Ubuntu 20.04 (16.04 to 19.10) also nautilus desktop font settings could be adjusted. To reset it run:

gsettings reset org.gnome.nautilus.desktop font

Hope it helps.

Ubuntu 15.10 and before

To reset the customization of gnome fonts done using System ⇒ Preferences ⇒ Appearance ⇒ Fonts use the following commands.

Basically these commands remove the customization by deleting the user instance of the gconf keys in which case the environment falls back to system defaults.

gconftool-2 --unset /desktop/gnome/interface/font_name
gconftool-2 --unset /desktop/gnome/interface/document_font_name
gconftool-2 --unset /desktop/gnome/interface/monospace_font_name
gconftool-2 --unset /apps/metacity/general/titlebar_font
gconftool-2 --unset /apps/nautilus/preferences/desktop_font 

Though the key identifiers end with name (at least in the first three instances) what is stored against them is the complete font spec (like family/font name, size, style etc).

Since these keys are stored inside your home directory they take effect in all ubuntu installations that share the home partition. The .gconf directory inside your home directory is where all this info is stored.

1. ~/.gconf/desktop/gnome/interface/%gconf.xml stores the info for
   • /desktop/gnome/interface/font_name
   • /desktop/gnome/interface/document_font_name
   • /desktop/gnome/interface/monospace_font_name
2. ~/.gconf/apps/metacity/general/%gconf.xml stores /apps/metacity/general/titlebar_font
3. ~/.gconf/apps/nautilus/preferences/%gconf.xml stores /apps/nautilus/preferences/desktop_font

So a crude way to reset the font info could be to temporarily rename/move these files. However this should be done when the user's gnome session is not active (thus from a tty session a la Ctrl+Alt+F1).

Of course these files have other keys in the same category that have nothing to do with font properties so moving the entire file would mean that the customizations for those are also lost. The way to deal key-wise is using gconftool-2 as mentioned above.

Copy and paste gconf-watcher into a file on your PC called gconf-watcher. Chmod it to executable. Run it in Terminal and leave it running.

Change each setting in in System → Preferences → Appearance → Fonts. Look at gconf-watcher's output to find out where it's stored in the gconf tree.

Now install gconf-editor. It looks and works a bit like the Windows Registry Editor. Use it to "unset" the relevant values. Know that "unset" really means "reset".

By the way, if I may ask, why is it that you'd like to reset the settings?