Debian systems (and perhaps others) have the following layout in /etc/apache2/
mods-available/ mods-enables/ sites-available/ sites-enabled/
The default setup has a tonne of files in both mods-available and sites-available, and then there are symlinks to those files in *-enabled/.
I've never bothered with the symlinks. I've always just moved the files.
I argue that this allows you to easily see which mods/sites have been enabled, and which have not. The symlinks only let you see which have been enabled (easily, anyway, without resorting to diff). However, my colleague believes differently.
So, what is The Right Way and why?