I don't think there is any EJB 2 to 3 migration tool, as Jeanne said. The general concepts remain the same, but EJB 3.x is a great step toward simplification and ease of development.
If your only concern is to upgrade your J2EE application server to a JEE5/JEE6 application server, you should not have to change anything: the EJB 3.1 specification supports backward compatibility.
On the other hand, if you're up for a full EJB 3.x migration of your application, I advise you to read Adam Bien's Real World Java EE Patterns Rethinking Best Practices. This book covers the changes between the core J2EE patterns and the way they can be rethought/removed using the new JEE programming style. It also provides a EJB 2 Integration and Migration strategy that can help you estimate the cost of your migration (the persistence layer will be the hardest) and choose between a EJB 2 to EJB 3 migration and a full rewrite of your application, provided you have access to the business needs and specification documents.