Etc/

etc/ is the place for most configuration files. There are many etc/ directories, and while they function the same, some of these directories are for specific purposes or override other etc/ directories. Most system start up commands and configuration settings go here.

/etc/

This is where system configuration files go. Most user customizations shouldn't go here, since this can be updated by system processes. This explains why a process may work temporarily after adjusting /etc/. Two such exceptions of custom files that belong here are the fstab and rc.conf.

/usr/local/etc/

System customized configurations belong here. These files override /etc/ files.

/compat/linux/etc/

These are where emulation configuration files belong, when /etc/ doesn't apply to these specific settings.