Evading the dotCMS ClassLoader (or any other ClassLoader), in this case because dotCMS contains a copy of jruby-1.3.1.jar and I need jruby-complete-1.6.5.1.jar, this example assumes the required additional plugin files are provided.

EvadeThatPeskyClassLoaderClassLoader.java

package test;

import java.net.URL;
import java.net.URLClassLoader;
import java.util.IdentityHashMap;
import java.util.Map;


// Sorry about the name, it was after 1AM when I came up with this class and the implementation...
public class EvadeThatPeskyClassLoaderClassLoader extends URLClassLoader {


	// These classes are our interface with the world outside this classloader, preferably classes that you control.
	// The classloader will return these classes when requested.
	// The use for them is that we can get instances that we can use without reflection.
	private final Class<?>[] bridgeClasses;

	public EvadeThatPeskyClassLoaderClassLoader(URL[] urls, Class<?> ... bridgeClasses) {
		super(urls, getSystemClassLoader());
		this.bridgeClasses = bridgeClasses;
	}

	@Override protected Class<?> loadClass(String name, boolean resolve) throws ClassNotFoundException {
		Map<Class<?>, Void> queue = new IdentityHashMap<Class<?>, Void>();
		Map<Class<?>, Void> processed = new IdentityHashMap<Class<?>, Void>();

		for (Class<?> c : bridgeClasses) {
			queue.put(c, null);
		}

		// Here we will traverse the entire
		while (!queue.isEmpty()) {
			Class<?> clazz = queue.keySet().iterator().next();
			queue.remove(clazz);
			if (processed.containsKey(clazz)) {
				continue;
			}
			processed.put(clazz, null);
			if (clazz.getName().equals(name)) {
				return clazz;
			}
			for (Class<?> i : clazz.getInterfaces()) {
				queue.put(i, null);
			}
			Class<?> sup = clazz.getSuperclass();
			if (sup != null) {
				queue.put(sup, null);
			}
		}

		// If none of the bridge classes, or their interfaces and superclasses match, load the class as we should.
		return super.loadClass(name, resolve);
	}

	// A simple helper method that ensures we load the right thing, to prevent class cast exceptions or pesky reflection.
	public <T> T initializeBridgeInstance(String implName, Class<T> bridgeClass) throws ClassNotFoundException, InstantiationException, IllegalAccessException {
		for (Class<?> c : bridgeClasses) {
			if (c == bridgeClass || bridgeClass.isAssignableFrom(c)) {
				Class<?> implClass = loadClass(implName);
				if (bridgeClass.isAssignableFrom(implClass)) {
					return bridgeClass.cast(implClass.newInstance());
				}
			}
		}
		throw new IllegalArgumentException(bridgeClass + " is not a bridge class (or superclass of one), as such you won't ever get a working instance.");
	}
}

FirstStage.java

package test;

import java.io.File;
import java.io.IOException;
import java.net.URL;

import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.jruby.Ruby;

// This servlet (add it to your web-ext.xml!) will
@SuppressWarnings("serial")
public class FirstStage extends HttpServlet {
	@Override
	protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
		// We determine some paths, this assumes that the tomcat directory of dotCMS is the working directory. Change the appropiate.
		final File pluginDir = new File("../plugins/JRubyTest").getAbsoluteFile();
		final File jrubyJar = new File(pluginDir, "lib/jruby-complete-1.6.5.1.jar");
		final File pluginJar = new File(pluginDir, "build/jar/plugin-JRubyTest.jar");

		System.out.println("Original SecondStage classloader: " + SecondStage.class.getClassLoader());
		System.out.println("Original Ruby classloader (the wrong one!): " + Ruby.class.getClassLoader());

		final EvadeThatPeskyClassLoaderClassLoader jRubyLoader = new EvadeThatPeskyClassLoaderClassLoader(new URL[]{jrubyJar.toURI().toURL(), pluginJar.toURI().toURL()}, JRubyInterface.class);
		try {
			JRubyInterface ruby = jRubyLoader.initializeBridgeInstance(SecondStage.class.getName(), JRubyInterface.class);

			ruby.createRuntime();
			try {
				ruby.eval("puts 'Hello from a happier jRuby world!'");
				ruby.eval("puts 'We will be requiring rubygems and compass next.'");
				ruby.eval("require 'rubygems';require 'compass'");
				ruby.eval("puts 'If we got here, then everything worked fine and we managed to load our version of jruby.'");
			} finally {
				ruby.terminate();
			}
		} catch (Throwable e) {
			throw new ServletException(e);
		}
		
		resp.getWriter().println("Guess it worked...");
	}
}

JRubyInterface.java

package test;

// Our bridge interface for JRuby
public interface JRubyInterface {
	void createRuntime();
	Object eval(String scriptlet);
	void terminate();
}

SecondStage.java

package test;

import java.io.File;
import java.util.Arrays;

import org.jruby.Ruby;
import org.jruby.RubyInstanceConfig;
import org.jruby.javasupport.JavaEmbedUtils;

// This is the 'second stage', an implementation of a bridge class
public class SecondStage implements JRubyInterface {
	{
		// This shows that we have a 'copy' of our desired classes.
		System.out.println("This: " + SecondStage.class.getClassLoader());
		System.out.println("Ruby: " + Ruby.class.getClassLoader());
	}

	private Ruby ruby;

	@Override
	public void createRuntime() {
		// Determine the lib directory for our plugin
		final File libPath = new File("../plugins/JRubyTest/lib");
		System.out.println("SecondStage.createRuntime(): " + libPath.getAbsolutePath());

		RubyInstanceConfig config = new RubyInstanceConfig();
		// Add the lib directory to the load path of JRuby
		config.loadPaths().add(libPath.getAbsolutePath());
		// Require the compass-gems jar, this is the jarred up contents of java -jar jruby-complete-1.6.5.1.jar -S gem install -i ./compass-gems compass
		config.requiredLibraries().add("compass-gems.jar");

		ruby = JavaEmbedUtils.initialize(Arrays.asList(), config);
	}

	@Override
	public void terminate() {
		JavaEmbedUtils.terminate(ruby);
	}

	@Override
	public Object eval(String scriptlet) {
		return ruby.evalScriptlet(scriptlet);
	}
}