Woops. I guess I recreated configuration management inside Org-mode. The Org file is where I think; the actual configs are just a byproduct of documentation.

I keep a quake.org file with snippets like this:

#+begin_src conf :tangle "~/.q2pro/base2q/autoexec.cfg"
name "winny"
#+end_src

When I invoke org-tangle (C-c C-v t), the files are updated from quake.org.

I don’t know if this is a good way to store configurations—but it works for me.