The JSP Target wizard creates a target in which you can build a Web application and helps you set deployment and configuration options for deploying the target to an application server.
The Web Site Target wizard creates a target for organizing the files for a Web site that can be deployed to ASP or to the file system.
The Source Controlled Web Target wizard opens a Web target that has been checked into a source control system.
For more information about creating Web applications, see Working with Web and JSP Targets.