Cosas varias con las que me tope cuando tuve que modificar la configuración de Apache.

Ejemplo en algunos casos tenemos un directorio autenticado

<Directory "/usr/local/nagios/share">
    AuthType    Basic
    AuthName    "Nagios Access"
    Options     All
    Order       allow,deny
    Allow       from all
    AllowOverride None
    AuthUserFile  /usr/local/nagios/etc/passwd.nagios
    require     valid-user
</Directory>

Pero a la vez dentro de el tenemos un directorio que no precisa privilegios y queremos que sea visible para los demas usuarios de la red sin necesidad de autenticación, para ello deberemos configurarlo de la siguiente manera :

<Directory "/usr/local/nagios/share/wiki">
    Options     +Indexes
    Satisfy     Any
    Allow       from All
    AllowOverride All
</Directory>

    RewriteEngine On
    RewriteCond %{HTTPS} off
    RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI}

Fragmento de configuración para Nagios

LDAPSharedCacheSize 200000
LDAPCacheEntries 1024
LDAPCacheTTL 600
LDAPOpCacheEntries 1024
LDAPOpCacheTTL 600

ScriptAlias /nagios/cgi-bin "/usr/local/nagios/sbin"

<Directory "/usr/local/nagios/sbin">
    SSLRequireSSL
    Options ExecCGI
    AllowOverride None
    Order allow,deny
    Allow from all
    AuthType               	Basic
    AuthName               	"Ingrese usuario y contraseña de Nagios"
    AuthBasicProvider 		ldap
    AuthLDAPURL 		"ldap://10.1.1.15:389/ou=users,dc=organizacion?uid"
    AuthLDAPURL 		"ldap://10.1.1.16:389/ou=users,dc=organizacion?uid"
    AuthLDAPBindDN 		uid=ldapadmin,ou=users,dc=organizacion
    AuthLDAPBindPassword 	123456
    Require 			valid-user
    Require group 		cn=linux-admin,ou=groups,dc=organizacion
</Directory>

En el blog sherekan http://sherekan.com.ar/2009/08/11/securizando-servidor-apache-parte-iv/ hay una nota simple sobre phpsu.

/etc/apache2/conf.d/security

#
# Disable access to the entire file system except for the directories that
# are explicitly allowed later.
#
# This currently breaks the configurations that come with some web application
# Debian packages. It will be made the default for the release after lenny.
#
#<Directory />
#	AllowOverride None
#	Order Deny,Allow
#	Deny from all
#</Directory>

# Changing the following options will not really affect the security of the
# server, but might make attacks slightly more difficult in some cases.

#
# ServerTokens
# This directive configures what you return as the Server HTTP response
# Header. The default is 'Full' which sends information about the OS-Type
# and compiled in modules.
# Set to one of:  Full | OS | Minimal | Minor | Major | Prod
# where Full conveys the most information, and Prod the least.
#
# En Prod no mostramos ninguna info de version ni nada
ServerTokens Prod

#
# Optionally add a line containing the server version and virtual host
# name to server-generated pages (internal error documents, FTP directory
# listings, mod_status and mod_info output etc., but not CGI generated
# documents or custom error documents).
# Set to "EMail" to also include a mailto: link to the ServerAdmin.
# Set to one of:  On | Off | EMail
#
# No mostrar info de version ni nada
ServerSignature Off

#
# Allow TRACE method
#
# Set to "extended" to also reflect the request body (only for testing and
# diagnostic purposes).
#
# Set to one of:  On | Off | extended
#
TraceEnable Off

/etc/php5/apache2/php.ini

expose_php = Off