If you are unfamiliar with the Web ADF, start with the introductory documentation. These topics will introduce you to JSF and give you an overview of the Web ADF. Next, the Getting Started topics, beginning with the Simple AGS Application, will walk you through the pieces of a Web ADF application and give you the foundation for beginning work on your own custom web application. There are also several sample applications, beginning with the ArcGIS Server Viewer, which can help you build further understanding of the concepts introduced in these documents. All the Web ADF samples are installed in /java/samples/server and are prefixed with webadf.

If you are familiar with the Web ADF then you can get started building your own application by taking the blank application found at <arcgis install location>/java/server/web/webcontrols and importing it into your favorite IDE. From there you can create a JSP page and start authoring an application. The Web ADF also includes a map viewer application found at  <arcgis install location>/java/server/web/web_map_application that provides a pre-configured application which can easily be extended into your own custom application. Run the arcgisant utility in the webtemplate directory and this will generate a WAR file which can be imported into your favorite IDE.

The Javadoc for the Web ADF and other reference documentation can be found in the reference section of the Table of Contents, starting with the Server library overview for the ArcObjects API.