Why is the HibernateException in Hibernate 3 a RuntimeException? It's strange to me that a failure to persist an object does not lead to a checked exception, forcing the client to handle the error. Does anyone else find this to be a problem?

It's a fatal exception, there is no point in forcing you to catch it, because all you can do is clean up and exit. Do this at the top of your call stack instead of in every method. Read the discussions in the Java community to understand this reasoning.