Following are all subdirectoires under /etc directory. Note that this subdirectories are first level and may contained more subdirectories. Following list is retrived on Red Hat Linux version 7.2.
Tip to see the complete list on your computer use command tree /etc

/etc
|-- X11
|-- alchemist
|-- cipe
|-- cron.d
|-- cron.daily
|-- cron.hourly
|-- cron.monthly
|-- cron.weekly
|-- default
|-- dhcpc
|-- dhcpcd -> dhcpc
|-- gnome
|-- gtk
|-- hotplug
|-- httpd
|-- init.d -> rc.d/init.d
|-- iproute2
|-- isdn
|-- kde
|-- locale
|-- log.d
|-- logrotate.d
|-- mail
|-- makedev.d
|-- midi
|-- mrtg
|-- nmh
|-- ntp
|-- openldap
|-- opt
|-- pam.d
|-- ppp
|-- profile.d
|-- rc.d
|-- rc0.d -> rc.d/rc0.d
|-- rc1.d -> rc.d/rc1.d
|-- rc2.d -> rc.d/rc2.d
|-- rc3.d -> rc.d/rc3.d
|-- rc4.d -> rc.d/rc4.d
|-- rc5.d -> rc.d/rc5.d
|-- rc6.d -> rc.d/rc6.d
|-- rpm
|-- samba
|-- security
|-- sgml
|-- skel
|-- smrsh
|-- snmp
|-- sound
|-- squid
|-- ssh
|-- sysconfig