To run LibreNMS under a subdirectory on your Apache server, the directives for the LibreNMS directory are placed in the base server configuration, or in a virtual host container of your choosing. If using a virtual host, place the directives in the file where the virtual host is configured. If using the base server on RHEL distributions (CentOS, Scientific Linux, etc.) the directives can be placed in /etc/httpd/conf.d/librenms.conf. For Debian distributions (Ubuntu, etc.) place the directives in /etc/apache2/sites-available/default.

#These directives can be inside a virtual host or in the base server configuration
AllowEncodedSlashes On
Alias /librenms /opt/librenms/html

<Directory "/opt/librenms/html">
    AllowOverride All
    Options FollowSymLinks MultiViews
</Directory>

The RewriteBase directive in html/.htaccess must be rewritten to reference the subdirectory name. Assuming LibreNMS is running at http://example.com/librenms/, you will need to change RewriteBase / to RewriteBase /librenms.

Finally, ensure $config["base_url"] -- if configured -- is correct as well.