After some moderate difficulty (mostly due to bugs 507536 and 552480) I have finally managed to setup Eclipse as a build environment for Apache Tomcat.  The process is as follows (Note that $DEVELSERVERDIR can be anything/anywhere that you have access to as a normal user):

1. aptitude install eclipse tomcat6-user
2. Install Java EE Development Tools plugin from the Eclipse WPT Project
3. tomcat6-instance-create $DEVELSERVERDIR
4. cd $DEVELSERVERDIR
5. ln -s /usr/share/tomcat6/lib
6. ln -s /usr/share/tomcat6/bin/bootstrap.jar bin
7. cp /var/cache/tomcat6/catalina.policy conf
8. Configure tomcat and eclipse to your liking and add the Tomcat instance to the Eclipse servers list

At this point you should be able to import/create projects which can be run on your local server instance. (If not, you are in the same boat I was in this morning... and best of luck to you)