So one of my colleagues whom is heavily involved in our current mapping project has been working with our polygons and trying to come up with some different solutions to make things faster, more scalable and workable. I networked with several people to try to find some fast easy workarounds and thanks to a couple of them pointing the way we were able to accomplish some things. With that, we loved the Java Topology Suite. Check out this post on the JTS and how we made things work.
http://webmonkeyswithlaserbeams.wordpress.com/2009/03/04/the-sweet-java-topology-suite-part-ii/
Enjoy
