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Update 2015: this is a very old question and a lot has changed in the past ~6 years. The JPA API's are quite feature-rich these days and I recommend using JPA since more and more tools and frameworks have aligned with it. One example is Spring Data JPA: it removes a lot of boilerplate for common tasks and is phenomenally productive:
http://projects.spring.io/spring-data-jpa/
Original Answer: I will echo cheng81's comments and also put in a vote for using the plain Hibernate APIs. The feature set of JPA is smaller than Hibernate's and I see no reason to handicap yourself with "pure JPA" just because it's a "standard."