This is more of a note to myself than anything else but might be helpful to others. Here are the config and data directories for Nagios when installed using packages on Ubuntu 12.04.
Config files
----------------------
/etc/nagios3/
/etc/nagios3/conf.d
/etc/nagios-plugins/config
/etc/nagios
Plugin executables
---------------------
/usr/lib/nagios/plugins
Graphing (pnp4naigos)
----------------------
/usr/share/pnp4nagios/html
/var/lib/pnp4nagios/perfdata
Other
-----------------------
/var/lib/nagios
/var/lib/nagios3
Here is a very simple backup script for Nagios on Ubuntu 12.04
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