Apache
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Apache offers a standard configuration for it's installation. Other companies are packaging additional services around Apache to provide additional product features, such as administration gui's. Covalent ERS is one of these product offerings. And additional iEngineers have developed their own ways of defining internet architectures. This is just one I like.

It should be noted this architecture was initially designed for Unix.
From the root:
  /www An organized root for your internet services
  /www/softlib
The standard location for all your web server library installations.
/www/softlib/modules
/www/softlib/apache-2.0.48
/www/softlib/jsdk-1.4
/www/softlib/modperl
/www/softlib/perl
/www/softlib/snmp
/www/softlib/tomcat-4.1.18
  /www/softlib/ - symbolic links -
Many iEngineers keep the previous version, and the next version of their internet software libraries on a server for testing or roll back needs. This also assists in the roll-out of new patches that can be made without affecting the current running version. Example:
/www/softlib/apache --> apache-2.0.47
/www/softlib/apache-2.0.46
/www/softlib/apache-2.0.47
/www/softlib/apache-2.0.48
/www/softlib/tomcat --> tomcat-4.1.12
/www/softlib/tomcat-4.1.12
/www/softlib/tomcat-4.1.18
  /www/softlib/modules Additional API's you might want/need to add on to your Apache installation. Managing these separate from Apache may keep you from replacing or losing modules that aren't standard with Apache's installations.
  /www/approot The standard location for you application libraries.
  /www/approot/application-name
The location of your TomCat applications. Example:
/www/approot/orders
/www/approot/scheduling
  /www/docroot The standard location for you document root libraries.
  /www/docroot/website-name
The location of your static or non-application sites and domains. Example:
/www/docroot/abc.com
/www/docroot/student1
/www/docroot/student2
  /www/servers The standard location of your independent web servers.
  /www/servers/-servername-
The location of your web server libraries. Example:
/www/servers/abc.com
/www/servers/springwolf.com
/www/servers/whatever.com
 
Each server library contains it's own version of the following:
../abc.com/bin
/startup
/startupssl
/stop
/restart
/snmp-start
/tomcat-start
../abc.com/conf
/catalina.policy
/httpsd.conf
/magic
/mime-types
/server.xml
/snmpd.conf
/startup.pl
/startup.properties
/tomcat-users.xml
/web.xml
/workers.properties
/wrapper.properties
/vhosts
/v-0080-abc.com
/v-2100-sales
../abc.com/logs
../abc.com/proxy
../abc.com/ssl
/ca-bundle.cert
/cacert.pem
/secure.cert
/secure.key
../abc.com/temp
../abc.com/var
/snmpd.local.conf
/wwwbucket.-servername-.dir
/wwwbucket.-servername-.pag
  /www/util The standard location of any home-grown utilities that may be added on to your services. Such as log rotation, automated file transfers for site or application implementations, and so on.