verified on RedHat 9, PHP 4.2.2
output from var_dump of array after openssl_x509_parse was performed. 
There should have been an ["OU"]=> "DoD" before the PKI line

["issuer"]=>
  array(4) {
    ["C"]=>
    string(2) "US"
    ["O"]=>
    string(15) "U.S. Government"
    ["OU"]=>
    string(3) "PKI"
    ["CN"]=>
    string(22) "DOD CLASS 3 EMAIL CA-7"

Multiple OUs are visible in "name" after openssl_x509_parse so here's a quick & dirty workaround:

function get_ous($data) {
    if (strlen(strstr($data,'/OU='))>0) {
        $parts=explode('=', $data);

        for ($i=0, $j=count($parts); $i<$j; $i++) {
            if ($i>0) {
                if (substr($parts[$i-1], strrpos($parts[$i-1], '/')+1)=='OU') {
                    $ret[]=substr($parts[$i], 0, strrpos($parts[$i], '/'));
                }
            }
        }
        return $ret;
    } else {
        return false;
    }
}

$cert=openssl_x509_parse($crt);
$ous=get_ous($cert['name']);
if (is_array($ous)) {
   //your code here
}

Here's my try for a patch that makes any multiple
entry (like multiple organisations) to be made into
arrays in the resulting array:

  http://www.php.net/~jani/patches/bug18613.patch

This bug has been fixed in CVS.

Snapshots of the sources are packaged every three hours; this change
will be in the next snapshot. You can grab the snapshot at
http://snaps.php.net/.
 
Thank you for the report, and for helping us make PHP better.