Earlier someone asked me how he could use windows cmd.exe with PHP. People run into trouble as soon as there are quotes needed because there are special characters (>/&()[]{}^=;!’+,`~ and ) in the command. I do it like this

<?php
$result = `""c:\\my path\\prog.exe" "filename""`;
?>

In case you have to do it often you might want to wrap it into a little function like this

<?php
function cmd($command, $arguments = null)
{
        $commandline = '';
        foreach(func_get_args() as $word) {
                $commandline .= '"' . $word . '" ';
        }
        $commandline = rtrim($commandline, ' ');
        $commandline = '"' . $commandline . '"';
        return `$commandline`;
}

// run blah.exe
cmd('blah.exe');

// run c:\my path\blah.exe with the arguments "foo" and "bar bar"
cmd('c:\\my path\\blah.exe', 'foo', 'bar bar');
?>