Essentially, it would be good if the installed gentoo java system packages (the output of "java-config -l") could be registered somehow in Eclipse, perhaps through the "User Libraries" component, allowing them to be easily added to the build path of any projects you are working on. After all, they are already installed on the system, they just need to be discovered.
Please see this script: http://dev.gentoo.org/~nelchael/bin/generate-userlibraries.sh
A nice script! :) It would be useful if it also searched /usr/share/doc/ for the package as well so that the javadoc location could be attached to the library. However, this script needs to be advertised more I think!