Well check out the Examinator Web Reference App. It's goal is to demonstrate and document everything from "Build and test" to "Deployment" for a high scale, realistic, web application. It strives to be well written and as simple as possible while still being a good demonstration of best practices. It also strives to document all the relivant pieces so others can learn from it. This is quite a challenge and I'm sure dissagreement will exist on some of the choices. I think it's an excellent start and the right set of goals.
Here is a taste of the stack and tools:
- Spring Webflow
- Spring MVC
- Spring Security
- Apache DBCP
- Apache mod_proxy
- Eclipse (+WTP)
It's pretty good now and I'm pretty sure it's going to get better and better over time so check in early and often. I hope others can learn as much from reading about it and hacking on it as we did writing it.