A source code encoder and a demonstration using it with PHP as a proof of concept

README.md

Create the encoded.java and the key like that:

java -jar Coder.jar -en original_code.php > encoded.txt

Code.java

package coder;

import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.security.InvalidKeyException;
import java.security.NoSuchAlgorithmException;
import java.security.spec.InvalidKeySpecException;
import java.util.Scanner;
import javax.crypto.Cipher;
import javax.crypto.IllegalBlockSizeException;
import javax.crypto.KeyGenerator;
import javax.crypto.NoSuchPaddingException;
import javax.crypto.SecretKey;
import javax.crypto.SecretKeyFactory;
import javax.crypto.spec.DESKeySpec;

/**
 *
 * @author periklis master_ex ntanasis - pntanasis@gmail.com
 */
public class Coder {

    // @see http://download.oracle.com/javase/1.4.2/docs/guide/security/jce/JCERefGuide.html#PBE
    //found here: http://www.exampledepot.com/egs/javax.crypto/DesString.html
    public static class DesEncrypter {

        Cipher ecipher;
        Cipher dcipher;

        DesEncrypter(SecretKey key) {
            try {
                ecipher = Cipher.getInstance("DES");
                dcipher = Cipher.getInstance("DES");
                ecipher.init(Cipher.ENCRYPT_MODE, key);
                dcipher.init(Cipher.DECRYPT_MODE, key);

            } catch (javax.crypto.NoSuchPaddingException e) {
            } catch (java.security.NoSuchAlgorithmException e) {
            } catch (java.security.InvalidKeyException e) {
            }
        }

        public String encrypt(String str) {
            try {
                // Encode the string into bytes using utf-8
                byte[] utf8 = str.getBytes("UTF8");

                // Encrypt
                byte[] enc = ecipher.doFinal(utf8);

                // Encode bytes to base64 to get a string
                return new sun.misc.BASE64Encoder().encode(enc);
            } catch (javax.crypto.BadPaddingException e) {
            } catch (IllegalBlockSizeException e) {
            } catch (UnsupportedEncodingException e) {
            } catch (java.io.IOException e) {
            }
            return null;
        }

        public String decrypt(String str) {
            try {
                // Decode base64 to get bytes
                byte[] dec = new sun.misc.BASE64Decoder().decodeBuffer(str);

                // Decrypt
                byte[] utf8 = dcipher.doFinal(dec);

                // Decode using utf-8
                return new String(utf8, "UTF8");
            } catch (javax.crypto.BadPaddingException e) {
            } catch (IllegalBlockSizeException e) {
            } catch (UnsupportedEncodingException e) {
            } catch (java.io.IOException e) {
            }
            return null;
        }
    }

    /** Save the specified TripleDES SecretKey to the specified file */
    public static void writeKey(SecretKey key, File f) throws IOException,
            NoSuchAlgorithmException, InvalidKeySpecException {
        // Convert the secret key to an array of bytes like this
        SecretKeyFactory keyfactory = SecretKeyFactory.getInstance("DES");
        DESKeySpec keyspec = (DESKeySpec) keyfactory.getKeySpec(key,
                DESKeySpec.class);
        byte[] rawkey = keyspec.getKey();

        // Write the raw key to the file
        FileOutputStream out = new FileOutputStream(f);
        out.write(rawkey);
        out.close();
    }

    /** Read a TripleDES secret key from the specified file */
    public static SecretKey readKey(File f) throws IOException,
            NoSuchAlgorithmException, InvalidKeyException,
            InvalidKeySpecException {
        // Read the raw bytes from the keyfile
        DataInputStream in = new DataInputStream(new FileInputStream(f));
        byte[] rawkey = new byte[(int) f.length()];
        in.readFully(rawkey);
        in.close();

        // Convert the raw bytes to a secret key like this
        DESKeySpec keyspec = new DESKeySpec(rawkey);
        SecretKeyFactory keyfactory = SecretKeyFactory.getInstance("DES");
        SecretKey key = keyfactory.generateSecret(keyspec);
        return key;
    }

    public static void main(String[] args) throws FileNotFoundException,
            NoSuchAlgorithmException, NoSuchPaddingException, IOException,
            InvalidKeySpecException, InvalidKeyException {

        if (args[0].equalsIgnoreCase("-en")) {
            Scanner in = new Scanner(new File(args[1]));

            String code = "";

            while (in.hasNext()) {
                code += in.nextLine() + "\n";
            }

            code = "?>" + code + "<?php";

            SecretKey key = KeyGenerator.getInstance("DES").generateKey();
            DesEncrypter encrypter = new DesEncrypter(key);

            writeKey(key, new File("key"));

            String encrypted = encrypter.encrypt(code);

            System.out.println(encrypted);
        } else if (args[0].equalsIgnoreCase("-de")) {
            Scanner in = new Scanner(new File(args[1]));

            String code = "";

            while (in.hasNext()) {
                code += in.nextLine() + "\n";
            }

            SecretKey key = readKey(new File(args[2]));
            DesEncrypter encrypter = new DesEncrypter(key);

            String decrypted = encrypter.decrypt(code);

            System.out.println(decrypted);
        }

    }
}

demo.php

<?php 

eval(shell_exec("java -jar Coder.jar -de encoded.txt key")); 

?>

encoded.txt
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key

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