In Eclipse Galileo (3.5) or Ganymede (3.4) or older version, you can control the project packaging structure via the “Java EE Module Dependencies” option, so that the project dependencies are deployed to the correct folder.

Eclipse-JavaEE-Module-Dependencies

However, in the latest Eclipse Helios (3.6), the “Java EE Module Dependencies” is replaced by “Web Deployment Assembly“, which provide more powerful and flexible ways to configure the project packaging structure.

Eclipse-Web-Deployment-Assembly
Note
See this Eclipse Web Tools Platform 3.2 announcement, just do not surprise when you can’t find the “Java EE Module Dependencies” option in your latest Eclipse IDE.