Today I had a strange deserialization problem with an EJB inside a BEA Weblogic server. It finally boiled down to classloading problem which was caused by a third party library. The library used the wrong class loader.
Some pittfalls which can happen with class loaders in an J2EE environments are described at "OnJava":http://www.onjava.com/pub/a/onjava/2004/06/30/classloader2.html