This week's book giveaway is in the Other Open Source APIs forum. We're giving away four copies of Storm Applied and have Sean Allen, Peter Pathirana & Matthew Jankowski on-line! See this thread for details.
They are tomcat/shared/lib and tomcat/shared/classes.
The hierarchy was simplified in version 6. I believe it's now just tomcat/lib
Be sure to read the release notes carefully. There is a section in there on JNI resources shared by multiple apps with some specific information on initializing them to insure that one app doesn't lock the others out.