There are 2 simpler (and much faster) methods for getting good getopt() operation without creating your own handler.
1. Use the Console_Getopt PEAR class (should be standard in most PHP installations) which lets you specify both short and long form options as well as whether or not arguments supplied to an option are themselves 'optional'. Very simple to use and requires very little code to operate compaired to writing own handler.
2. If you cannot load external PEAR objects, use your shell's getopt() functions (which in BASHs case work very well) to process options and have your shell script then call your PHP script with a rigid argument structure that is very easy for PHP to digest such as:
% myfile.php -a TRUE -b FALSE -c ARGUMENT ...
If the initial arguments are invalid you can have the shell script return an error without calling the PHP script. Sounds convoluted but is a very simple solution and in fact PHP's own % pear command uses this method. /usr/bin/pear is a shell script that does some simle checking before calling pearcmd.php and repassing the arguments on to it.
The second method is by far the best for portability because it allows a single shell script to check a few things like your PHP version and respond acordingly e.g. does it call your PHP4 or PHP5 compatible script? Also, because getopt() is not available on Windows, The second solution allows you to do Windows specific testing as a BAT file (as oposed to BASH, ZSH or Korn on UNIX).