Deployment Descriptor Purgatory
It's not quite as bad as "DLL Hell", but I just spent the past 2 hours trying to track down a bug in my Java code only to find out the root cause was due to a mis-configured element in one of the many and multitudonous deployment descriptor XML files on my Web Container.
There's definitely something to the new lightweight movement afoot in J2EE-land. Note to self (and others) Check-out the design patterns used in Rails to see how applicable they are to non-Ruby implementations. It seems like Rails has taken the DRY (Do not Repeat Yourself) philosophy to the extreme.