I've never created a proper java web application besides a simple java app that's just embedded into a html page.
A simple breakdown of a java web application that I came across whilst reading the Java EE Tutorial was:
A web application consists of web components (either Java servlets, JSP pages or web service endpoints), static resource files such as images, and helper classes and libraries. The web container provides many supporting services that enhance the capabilities of web components and make them easier to develop. However, because a web application must take these services into account, the process for creating and running a web application is different from that of traditional stand-alone Java classes.
The process for creating, deploying, and executing a web application can be summarized as follows:
1. Develop the web component code.
2. Develop the web application deployment descriptor.
3. Compile the web application components and helper classes referenced by the components.
4. Optionally package the application into a deployable unit.
5. Deploy the application into a web container.
6. Access a URL that references the web application.