Apache
Webmin is a web-based interface for system administration for Unix. Using any modern web browser, you can setup user accounts, Apache, DNS, file sharing and much more. Webmin removes the need to manually edit Unix configuration files like /etc/passwd, and lets you manage a system from the console or remotely. See the standard modules page for a list of all the functions built into Webmin, or check out the screenshots.
There is also apacheConf.
ApacheConf is the progam that can configure the remote Apache servers on Linux machines. It will help you to tune the main Apache configuration httpd.conf file on Linux. ApacheConf presents all the information in the httpd.conf file in a structured view. All of the server's directives are grouped by category (Global parameters, Main server's parameters, Directories, Virtual hosts, etc) and all these groups are represented as a tree. In this way, you can see the entire structure of the server on Linux computer at a glance and you can easily manage all of the server's directives, as well as the directories and virtual hosts.
It has some cave-ats: it implements its own structure and ignores any Ubuntu specific configuration and you are bound to the GUI (if it is not implemented into the GUI...)
MySQL
For MySQL I would suggest MySQL Workbench. There is a special APT repo for MySQL Workbench. From the link:
The MySQL APT repository provides a simple and convenient way to
install and update MySQL products with the latest software packages
using Apt.
The APT repository supports the following Linux Distros:
Debian - 7
Ubuntu - 12.04 LTS
Ubuntu - 14.04 LTS
Ubuntu - 14.10
MySQL APT repository includes the latest packages:
MySQL 5.6 (GA)
MySQL 5.7 (Development Release)
MySQL Workbench 6.2 (GA) - Ubuntu Only
MySQL Connector / Python
PHP
There probably is not a lot for PHP besides the "phpinfo()" function you can add to a webpage and show anything loaded. Example from the link:
<?php
// Show all information, defaults to INFO_ALL
phpinfo();
// Show just the module information.
// phpinfo(8) yields identical results.
phpinfo(INFO_MODULES);
?>
Save it in your root as "phpinfo.php" and point your browser to it (ie. http://localhost/phpinfo.php)