Bootstrapping Magento by calling:

require_once 'app/Mage.php';
Mage::app();
// Your code

This is the simplest way but not really the Magento way because we're not using class that extends Mage_Shell_Abstract - the class which when extended provides us with tools to parse command line arguments, calls __applyPhpVariables() in it's constructor (function parses .htaccess files and applies php settings to shell script).

Magento way

File resides in shell/custom.php

<?php
require_once' abstract.php';

class Stackoverflow_Shell_Custom extends Mage_Shell_Abstract
{

protected $_argname = array();
 
    public function __construct() {
        parent::__construct();
 
        // Time limit to infinity
        set_time_limit(0);     
 
        // Get command line argument named "argname"
        // Accepts multiple values (comma separated)
        if($this->getArg('argname')) {
            $this->_argname = array_merge(
                $this->_argname,
                array_map(
                    'trim',
                    explode(',', $this->getArg('argname'))
                )
            );
        }
    }

 // Shell script point of entry
    public function run() {
 
    }
 
    // Usage help
    public function usageHelp()
    {
        return <<<USAGE
Usage:  php -f scriptname.php -- [options]
 
  --argname <argvalue>       Argument description
 
  help                   This help
 
USAGE;
    }
}
// Instantiate
$shell = new Stackoverflow_Shell_Custom();
 
// Initiate script
$shell->run();

}

View Status:

php indexer.php status

Reindex All

php indexer.php reindexall

Reindex Specific Index

php indexer.php --reindex CODE (see list below)

List of Individual Codes