What should be the preferred choice for O/R mapping...?
These frameworks provide similarly common features:
EntityManager - A transaction-level artifact that references, maintains identity and manages the objects in a given transaction. JDO calls this a PersistenceManager, Hibernate calls this a Session. TopLink calls this a UnitOfWork. These are all very close in scope, purpose and API.
Named queries - Queries must be able to be pre-defined and bound to a name for later retrieval and execution. These are called named queries in all of TopLink, Hibernate and JDO.
Native queries - Native SQL queries that allow the application to specify the query criteria in SQL. These are called SQL queries in all of TopLink, Hibernate and JDO.
Callback Listeners - The ability to define a class or method that will get invoked when a given event occurs. TopLink calls these event listeners, Hibernate and JDO call them life cycle callbacks.
Detaching/Reattaching objects - Objects can leave the scope of the EntityManager that controls them. They can also be reattached to the same or a different EntityManager through the use of the merge API call on the EntityManager. TopLink offers a series of merge calls, the most basic one being mergeClone. Hibernate has saveOrUpdateCopy and JDO has a couple of flavours of attachCopy call on the PersistenceManager.
O/R Mapping Types - All of the direct and relationship mapping types that are fundamental to mapping object state to relational database tables. These are all supported by Hibernate, TopLink and JDO. I won't go through all of the names (one-to-one, etc.. they are all pretty standard), but although some of the names differ a little bit from one to the other the functionality is pretty much the same and what you would expect.
Embedded Objects - Objects that have no persistent identity of their own but depend upon their parent object for identity. JDO calls them embedded objects, TopLink calls them aggregates and Hibernate calls them components.