When you undeploy a webapp, ideally it should go away and its WebAppClassLoader should be garbage collected. There are various reasons this won't happen, but they essentially split into two problems:
1) The App Server has references to classes in the WebAppClassLoader in its own objects (on Tomcat these are typically commons logging statics in StandardContext in catalina, or some of the jakarta code). There's not much you can do about this, short of getting a better app server.
2) You hold references to Class objects loaded by your WebAppClassLoader in static fields in other Classes loaded by your WebAppClassLoader.
Number 2 can be solved by the use of WeakReferences to the Class objects.
Note that you also need to be careful about classes that have Class references internally, such as java.lang.reflect.Method and Field. You can also hold these items in a WeakReference, but they have the potential to be garbage collected randomly, unlike the underlying Class objects.
I have some patches that allow me to start up and shut down a Spring-backed Wicket-based app and have the classloader cope properly. They could probably do with some review.