Bueno como muchos sabrán existe un programa llamado JCrypt el cual encripta un jar y lo carga en runtime, algo diferente a lo que hago yo al momento de cargar clases, pues navegando un poco encontre esto que me imagino que fue donde se baso para hacer tal programa XD

Fuente:
[Enlace externo eliminado para invitados]

import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.Hashtable;

/**
 * Demonstration of a ClassLoader
 */
public class ClassLoaderDemo1 extends ClassLoader {
  /** The Hashtable to keep track of classes, to avoid re-loading them */
  protected Hashtable cache = new Hashtable();

  /** data's expected length */
  private final int dataLength = 433;

  /** data, obtained by dumping a compiled .class file */
  private int[] data = { 202, 254, 186, 190, 0, 3, 0, 45, 0, 31, 8, 0, 20, 7,
      0, 17, 7, 0, 25, 7, 0, 26, 7, 0, 27, 10, 0, 4, 0, 9, 9, 0, 5, 0,
      10, 10, 0, 3, 0, 11, 12, 0, 14, 0, 12, 12, 0, 28, 0, 22, 12, 0, 29,
      0, 13, 1, 0, 3, 40, 41, 86, 1, 0, 21, 40, 76, 106, 97, 118, 97, 47,
      108, 97, 110, 103, 47, 83, 116, 114, 105, 110, 103, 59, 41, 86, 1,
      0, 6, 60, 105, 110, 105, 116, 62, 1, 0, 4, 67, 111, 100, 101, 1, 0,
      13, 67, 111, 110, 115, 116, 97, 110, 116, 86, 97, 108, 117, 101, 1,
      0, 4, 68, 101, 109, 111, 1, 0, 9, 68, 101, 109, 111, 46, 106, 97,
      118, 97, 1, 0, 10, 69, 120, 99, 101, 112, 116, 105, 111, 110, 115,
      1, 0, 10, 72, 101, 108, 108, 111, 32, 74, 97, 118, 97, 1, 0, 15,
      76, 105, 110, 101, 78, 117, 109, 98, 101, 114, 84, 97, 98, 108,
      101, 1, 0, 21, 76, 106, 97, 118, 97, 47, 105, 111, 47, 80, 114,
      105, 110, 116, 83, 116, 114, 101, 97, 109, 59, 1, 0, 14, 76, 111,
      99, 97, 108, 86, 97, 114, 105, 97, 98, 108, 101, 115, 1, 0, 10, 83,
      111, 117, 114, 99, 101, 70, 105, 108, 101, 1, 0, 19, 106, 97, 118,
      97, 47, 105, 111, 47, 80, 114, 105, 110, 116, 83, 116, 114, 101,
      97, 109, 1, 0, 16, 106, 97, 118, 97, 47, 108, 97, 110, 103, 47, 79,
      98, 106, 101, 99, 116, 1, 0, 16, 106, 97, 118, 97, 47, 108, 97,
      110, 103, 47, 83, 121, 115, 116, 101, 109, 1, 0, 3, 111, 117, 116,
      1, 0, 7, 112, 114, 105, 110, 116, 108, 110, 1, 0, 4, 116, 101, 115,
      116, 0, 33, 0, 2, 0, 4, 0, 0, 0, 0, 0, 2, 0, 9, 0, 30, 0, 12, 0, 1,
      0, 15, 0, 0, 0, 37, 0, 2, 0, 0, 0, 0, 0, 9, 178, 0, 7, 18, 1, 182,
      0, 8, 177, 0, 0, 0, 1, 0, 21, 0, 0, 0, 10, 0, 2, 0, 0, 0, 9, 0, 8,
      0, 8, 0, 1, 0, 14, 0, 12, 0, 1, 0, 15, 0, 0, 0, 29, 0, 1, 0, 1, 0,
      0, 0, 5, 42, 183, 0, 6, 177, 0, 0, 0, 1, 0, 21, 0, 0, 0, 6, 0, 1,
      0, 0, 0, 7, 0, 1, 0, 24, 0, 0, 0, 2, 0, 18 };

  /** "load", that is, make up, the data for the class */
  private byte[] genClassData(String name) {
    if (dataLength != data.length)
      throw new IllegalArgumentException("data corrupt");
    byte[] bd = new byte[data.length];
    for (int i = 0; i < bd.length; i++)
      bd[i] = (byte) data[i];
    return bd;
  }

  public synchronized Class loadClass(String name, boolean resolve)
      throws ClassNotFoundException {
    /**
     * We can expect to be called to resolve at least demo's superclass
     * (java.lang.Object). Fortunatetely, we can just use
     * super.findSystemClass() to load such things...
     */
    if (name.startsWith("java.")) {
      System.out.println("loadClass: SystemLoading " + name);
      return findSystemClass(name);
    }
    Class c = (Class) cache.get(name);
    if (c == null) {
      System.out.println("loadClass: About to genClassData " + name);
      byte mydata[] = genClassData(name);
      System.out.println("loadClass: About to defineClass " + name);
      c = defineClass(name, mydata, 0, mydata.length);
      System.out.println("loadClass: storing " + name + " in cache.");
      cache.put(name, c);
    } else
      System.out.println("loadClass: found " + name + " in cache.");
    if (resolve) {
      System.out.println("loadClass: About to resolveClass " + name);
      resolveClass(c);
    }
    return c;
  }

  public static void main(String[] argv) {
    System.out.println("ClassLoaderDemo1 starting");
    ClassLoaderDemo1 loader = new ClassLoaderDemo1();
    Class c = null;
    Object demo;
    try {
      /* Load the "Demo" class from memory */

      System.out.println("About to load class  Demo");
      c = loader.loadClass("Demo", true);
      System.out.println("About to instantiate class Demo");
      demo = c.newInstance();
      System.out.println("Got Demo class loaded: " + demo);

      /* Now try to call a method */

      Method mi = c.getMethod("test", null);
      mi.invoke(demo, null);

    } catch (InvocationTargetException e) {
      // The invoked method threw an exception. We get it
      // wrapped up inside another exception, hence the
      // extra call here:
      e.getTargetException().printStackTrace();
      System.out.println("Could not run test method");
    } catch (Exception e) {
      e.printStackTrace();
      System.out.println("Could not run test method");
    }

    /**
     * Try to load some arbitrary class, to see if our ClassLoader gets
     * called.
     */
    System.out.println("Trying to load an unrelated class");
    java.awt.image.DirectColorModel jnk = new java.awt.image.DirectColorModel(
        24, 8, 8, 8);
    System.out
        .println("Load an unrelated class - was your ClassLoader called?");

    /** Try to instantiate a second ClassLoader */
    System.out.println("Trying to install another ClassLoader");
    ClassLoaderDemo1 loader2 = new ClassLoaderDemo1();
    System.out.println("Instantiated another ClassLoader...");
  }
}

Lo que hace es que carga una clase (ejemplo: archivo.class ) que fue dumpeado anteriormente y lo ejecuta en memoria usando Reflexion.

Con este code se puede modificar perfectamente para hacer un cripter para aplicaciones en java.
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