Do you have an X11 application that insists on using a font you hate?

Change that easily with fontconfig.

This syntax in your .fonts.conf will change the response for one font into an answer from another:

<alias>
 <family>Gentium</family>
 <prefer>
  <family>Tex Gyre Pagella</family>
 </prefer>
</alias>

Add as many stanzas as you like; then run fc-cache and restart your application.