3.3 is the first release using Maven as the build tool and using the notion of modules.

You may also want to look at the Hibernate Core Migration Guide : 3.2.

Specific migration concerns include:

New Second-level Caching SPIs

The old CacheProvider interfaces/impls are still around with bridges to the new APIs, so this is more of a heads-up. Currently only the integration with JBossCache 2.x via the hibernate-jbosscache2 module takes advantage of the new SPIs.

slf4j

Hibernate has migrated to using slf4j as the logging framework.  A significant difference between the two is that slf4j requires that users (at least) select which logging backend they want to use. This is accomplished by defining a dependency on the appropriate logging bridge (slf4j-log4j for example) if using maven or by dropping any needed jars on your classpath. See Steve's module blog entry for details.

javassist

Javassist is now the default bytecode provider rather than cglib.

Modularization

Again see Steve's module blog entry for details.