Spring Security. Although it is branded as Spring, you might find it useful for web applications; do note that you don't need to write a Spring app to use Spring Security.
If you wish to stick to JAAS, I would suggest using one of the container's login modules, just to get started, before you attempt to write your own login module. Be forewarned that you might end up writing one, if the container supplied modules do not meet your requirements. And, there is a good book on JAAS to help you understand it in detail.
Moreover, take a look at Servlet spec 3.0, to see how annotations can be used declare the roles (@DeclareRoles, which came in servlet spec 2.5) in the servlet itself, before defining what roles have access to what HTTP method (using @RolesAllowed). You can also employ annotations like @DenyAll and @PermitAll, to permit or forbid access to all users. @TransportProtected will ensure that the HTTP method is accessed over HTTPS. All one needs to do, is to map these roles in the source code, to actual roles in the JAAS realm; this often done using a container specific descriptor file.
ADDENDUM
Since you are using JSPs and not Facelets or any other technology for the presentation tier, you might be interested in the JSP tags offered by Spring Security. It is much cleaner that maintaining all of the authorization metadata in a humongous web.xml file.
As far as JPAs are concerned, well, the underlying access to them is usually enforced at the servlets or EJBs. Of course, you can build in more programmatic security, based on your needs - using entity listeners would help in this process as you would be able to intercept load, update and persist operations (if you are that particular, but for the most part building security before your business logic is executed usually is sufficient).
And oh, take a look at JBoss Seam (and Seam security), for it is a complete application development framework built on Java EE.