Custom command line tools can be added through the IDE Settings | Command Line Tool Support pane in PhpStorm. We can define commands, parameters and help information for our custom command line tool via special XML file. After saving the XML file containing the description for a specific custom tool, PhpStorm will recognize the command and provide us with autocompletion for our custom command line tool. Check a full tutorial here.
TYPO3 Flow command line tool
Developer tool for Magento developers
Scorprio Framework command line tool
AppFog command line tool
Windows Azure CLI
Windows Azure CLI tools autocompletion for PhpStorm
Zend Server's deployment tool (zdpack)
Zend Sever's deployment command line tool (zdpack)
Did you find other Custom Tools Command Definitions or did you create one for your own framework? Provide us with a link in twitter and we'll add them to the list.