For .Net there are lots of projects that Microsoft/others provide via which one can learn how patterns etc. are implemented in real life projects.
I am looking for ones for J2EE (apart from the samples that Sun provides on:http://java.sun.com/javaee/reference/code/). Am looking for more complex ones. May be using JSF/Spring/Struts
There are several. One possibility is the AppFuse project. It gives you some options to choose frameworks and see a full app generated. You can start here.
The Java Pet Store demo is a reference application using JSF. It's referenced on the page at the bottom, but it's hidden away at the bottom. This, and the Java BluePrints project, are a good reference about patterns in a decent sized project.
Sun provides BluePrints (with the famous Pet Store and the Adventure Builder applications) that show patterns and how they can be implemented using JEE APIs. About the Java PetStore 2.0:
The Java Pet Store 2.0 is the reference application for building AJAX web applications on Java EE 5. It illustrates BluePrints for using AJAX with Java, building AJAX-enabled JSF component libraries, using Java Persistence APIs, applying MVC and other design patterns in an AJAX web app, using Mashups such as Google Maps service for location specific searches of pets and PayPal service for purchases, using an RSS feed as a data source, and lots more.
Note that for versions prior to JEE 5, I really don't think one should consider them as representative of best/good practices but only as technology showcases. JEE 5 has made things much better.
Still, you should have a look at Spring's PetStore sample application (which illustrates iBATIS integration if I remember well) too. It's definitely worth the check.
And you may found others samples like this one (and many others, just google for "Java PetStore").