As the software installation process is somewhat different in Gentoo Linux, let's see how Apache is installed and PHP is enabled, and later on an application is deployed.
USE="cgi cli apache2" emerge --ask apache php
Now apache2 should be installed, with /etc/init.d/apache2 as an initscript and /var/www as its document root.
We want to enable PHP:
$ grep ^APACHE2_OPTS /etc/conf.d/apache2 APACHE2_OPTS="-D DEFAULT_VHOST -D INFO -D SSL -D SSL_DEFAULT_VHOST -D LANGUAGE -D PHP5"
That way the "IfDefine PHP5" in /etc/apache2/modules.d/70_mod_php5.conf will take effect and load the libphp5.so module.
As an example, let's install Nagios:
USE="png jpeg" emerge media-libs/gd
sed 's/for file in includes\/rss.*\/\*/&.*/' -i.orig html/Makefile.in
useradd -U -s /bin/sh -d /opt/nagios -g nagios nagios ./configure --prefix=/opt/nagios --with-httpd-conf=/etc/apache2/vhosts.d make all make install install-cgis install-init install-config install-webconf