The /etc directory contains most of the configuration files for your system. Some may be in /etc and some may have made their own directory (/etc/apache, for example). An important directory is /etc/init.d. It contains several scripts that Linux runs through during startup. You can start|stop|restart these yourself by typing /etc/init.d/file action. For example: "/etc/init.d/gpm stop". You may only need to restart these if you change their configuration file[s].
Dot Files
Dot files are files that start with a ".". An example is the file "/root/.bash_profile". All files starting with a dot are hidden, so you will have to use the "-a" option in "ls" (type: ls -a) in order to see them. Programs may store their configuration in your home directory this way. This allows different users on your system to have different settings for the same program, what a novel idea.
Advanced Topics