You can easily parse command line arguments into the $_GET variable by using the parse_str() function.
<?php
parse_str(implode('&', array_slice($argv, 1)), $_GET);
?>
It behaves exactly like you'd expect with cgi-php.
$ php -f somefile.php a=1 b[]=2 b[]=3
This will set $_GET['a'] to '1' and $_GET['b'] to array('2', '3').
Even better, instead of putting that line in every file, take advantage of PHP's auto_prepend_file directive. Put that line in its own file and set the auto_prepend_file directive in your cli-specific php.ini like so:
auto_prepend_file = "/etc/php/cli-php5.3/local.prepend.php"
It will be automatically prepended to any PHP file run from the command line.