Matt Simmons wrote this howto for Nagios. It covers how to organize your configuration directory in a way that makes it easier (in Matt’s opinion) to add new hosts, groups, services, and commands in a logical manner.
Here is a link to his website:
http://www.standalone-sysadmin.com/blog/2009/07/nagios-config/
Whoever caught this, thank you very much for the link! I hope you found it informative and useful.