Below is a proof of concept to sign php files with inline S/MIME signatures.

{{{
#!/usr/bin/php -q
<?
        $key = "client.key";
        $crt = "client.crt";
        $infile = $argv['1'];
        $outfile = $argv['2'];

        if($argc != 3)
        {
                die("Usage: $argv[0] <input file> <output file>\n");
        }

        $return = trim(`openssl smime -sign -signer $crt -inkey $key -in $infile`);

        $lines = explode("\n", $return);

        $bits = explode(";", $lines['1']);
        $bits = explode("=", $bits['3']);
        $boundary = substr($bits['1'], 1, -1);

        foreach($lines as $line)
        {
                if($open == 1 && $line == "--".$boundary)
                {
                        $open = 0;
                        $closed = 1;
                }

                if($file != "")
                        $file .= "\n";

                if($open == 1)
                        $file .= $line;
                else
                        $file .= "//".$line;

                if($open == 0 && $line == "--".$boundary && $closed != 1)
                        $open = 1;
                if($closed == 1)
                        $closed = 0;
        }

        $file = "<?php\n".$file."\n?>";

        $fp = fopen($outfile, "w");
        fputs($fp, $file);
        fclose($fp);
?>
}}}

Example output:
{{{
<?php
//MIME-Version: 1.0
//Content-Type: multipart/signed; protocol="application/x-pkcs7-signature"; micalg=sha1; boundary="----CCE07ED9FDA29AA9AAF3E3BB13BC40D8"
//
//This is an S/MIME signed message
//
//------CCE07ED9FDA29AA9AAF3E3BB13BC40D8
<?
        echo "Hello World!<br>\n";
?>

//------CCE07ED9FDA29AA9AAF3E3BB13BC40D8
//Content-Type: application/x-pkcs7-signature; name="smime.p7s"
//Content-Transfer-Encoding: base64
//Content-Disposition: attachment; filename="smime.p7s"
//
//MIIHfgYJKoZIhvcNAQcCoIIHbzCCB2sCAQExCzAJBgUrDgMCGgUAMAsGCSqGSIb3
//4co0IHqCtNvoAZRbdThgRX1Ww2cdJu8dFKXXzRdmbCsJKndQVsvM3sKxETkP7PaE
//54Y=
//
//------CCE07ED9FDA29AA9AAF3E3BB13BC40D8--
?>
}}}

this is an other version of the script above. This version wraps both signing parts in own <?php ?> tags. Feel free to send feedback to the author (Frank Nägler) or wrote some comments to this wiki page.

{{{
#!/usr/bin/php -q
<?php
	// @author Frank Nägler <mail (AT) naegler.net>
	// 29.06.2008
	$key		= "client.key";
	$crt		= "client.crt";
	$infile		= $argv['1'];
	$outfile	= $argv['2'];

	if ($argc != 3) {
		die("Usage: $argv[0] <input file> <output file>\n");
	}

	$return = trim(`openssl smime -sign -signer $crt -inkey $key -in $infile`);
	$lines = explode("\n", $return);

	$bits = explode(";", $lines['1']);
	$bits = explode("=", $bits['3']);
	$boundary = substr($bits['1'], 1, -1);
	$firstPart   = '';
	$middlePart  = '';
	$lastPart    = '';
	$inFirstPart = true;
	$inLastPart  = false;

	foreach ($lines as $line) {
		if ($inFirstPart) {
			$firstPart[] = $line;
			if ($line == '--'.$boundary) {
				$inFirstPart = false;
				continue;
			}
		}

		if ($line == '--'.$boundary) {
			$inLastPart = true;
		}
		
		if ($inLastPart) {
			$lastPart[] = $line;
		}
		
		if (!$inFirstPart && !$inLastPart) {
			$middlePart[] = $line;
		}
	}

	$file = "<?php\n// " . implode("\n// ", $firstPart) . "\n?>\n";
	$file .= implode("\n", $middlePart);
	$file .= "<?php\n// " . implode("\n// ", $lastPart) . "\n?>";

	$fp = fopen($outfile, "w");
	fputs($fp, $file);
	fclose($fp);
?>
}}}

Example output:
{{{
<?php
// MIME-Version: 1.0
// Content-Type: multipart/signed; protocol="application/x-pkcs7-signature"; micalg=sha1; boundary="----CCE07ED9FDA29AA9AAF3E3BB13BC40D8"
// 
// This is an S/MIME signed message
// 
// ------CCE07ED9FDA29AA9AAF3E3BB13BC40D8
?>
<?
        echo "Hello World!<br>\n";
?>
<php
// ------CCE07ED9FDA29AA9AAF3E3BB13BC40D8
// Content-Type: application/x-pkcs7-signature; name="smime.p7s"
// Content-Transfer-Encoding: base64
// Content-Disposition: attachment; filename="smime.p7s"
// 
// MIIHfgYJKoZIhvcNAQcCoIIHbzCCB2sCAQExCzAJBgUrDgMCGgUAMAsGCSqGSIb3
// 4co0IHqCtNvoAZRbdThgRX1Ww2cdJu8dFKXXzRdmbCsJKndQVsvM3sKxETkP7PaE
// 54Y=
//
// ------CCE07ED9FDA29AA9AAF3E3BB13BC40D8--
?>
}}}

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 . CategorySoftware