It depends. If you will be using Java EE, don't worry about Hibernate versions and focus on JPA 2.0. Hibernate will be just a JPA implementation. In case you really need a specific Hibernate function, check its version based on your AS implementation.
If you are not using Java EE, I would go with Hibernate 3.6 if I plan to deploy my application in a few months, or I would use 3.5 if I plan to deploy the application to production next week.
The main idea: to use the latest GA at a time when you put something in production. In this way, you guarantee that you will have a “supported” version for a long time.
It is also worth mentioning that community versions are not always supported by the provider. In this case, you will not receive a support contract from Red Hat for Hibernate 3.5 or 3.6. If you need support, you will have to choose any versions that they officially support.
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