App server PermGen errors that happen after multiple deployments are most likely caused by references held by the container into your old apps' classloaders. For example, using a custom log level class will cause references to be held by the app server's classloader. You can detect these inter-classloader leaks by using modern (JDK6+) JVM analysis tools such as jmap and jhat to look at which classes continue to be held in your app, and redesigning or eliminating their use. Usual suspects are databases, loggers, and other base-framework-level libraries.
See Classloader leaks: the dreaded "java.lang.OutOfMemoryError: PermGen space" exception, and especially its followup post.