Java based web applications need to run inside of a web container such as Jetty or Tomcat.
You build your app and deploy it to the container which hosts the application at runtime.
Pure/plain JDBC should only be used directly by simple applications or integration layers that do not have access to the class model.
Most applications that I have seen have used some kind of Object Relational Mapping framework which models the entities as classes at a higher level than plain old JDBC.
Popular O/R frameworks include:
For web based development, you could start with AppFuse, see the quickstart guide.
AppFuse is a templating system that generates the skeleton of an application for you.
Then look deeper into what has been generated, and see what frameworks they are using.
AppFuse lets you choose between different technology stacks, so you could compare.
I haven't see AppFuse support for Guice or GWT.
Guice is a Dependency Injection framework, others that could be used instead are Spring or picocontainer.
Another investigative approach that you could try would be starting with AndroMDA, which is a model driven architecture framework - you start with a UML model and then generate or forward engineer a working application.
AndroMDA also lets control the choice of the underlying framework implementations by configuring different cartridges, once again you should dig deeper to see what they are using in the generated application.