Many of u will agree that learning from open source project is another way of improving programming skills .Can me make list of open source applications that best demonstrates the use of layer architecture.
I guess JBoss is a good example of multiple layers Architecture...
alt text http://www.jboss.com/images/appInstrumentation.gif
I'm not sure it fits exactly your needs, but the source code of Ignite Realtime's Openfire Server is really nicely organized. It was a pleasure to modify its source to the needs of a company I worked for a few years ago.
It depends on what kind of application you would like to see. I find Kigg a good example of layered architecture, if we talk about a web application. It is written in asp.net mvc and has a nice separation of concerns\responsibilities.