.NET has codeplex for good sample applications to understand best practices. In Java, the first level of difficulty lies in finding a project with the frameworks you are interested to see implemented. In any case I've been unsuccessful in finding sample applications.
SourceForge.NET has many, but a lot of them are incomplete. Many other samples I find are only covering a CRUD - like Spring web site provides a CRUD, struts 2 provides a CRUD and I found some more here: http://www.learntechnology.net/content/main.jsp
None of them cover an application with decent level of complexity. I'm sure there are such projects, it's just my inability to find them.
Can someone provide the key for the treasure :-)
Edit: I got a comment asking me for specifics, so here it is:
I'm looking for a web application, built with a framework like Struts 2, Spring MVC (any action framework basically), Hibernate / Plain JDBC / JDBC templates in Spring at DAL, and no EJB's please!!
An application like bug tracker, blog template, inventory management etc.. anything that is non-trivial.