Do not close this as a duplicate of other questions because I'm not asking the same thing. They're also about a year old. That said, see these links:
http://db.apache.org/jdo/jdo_v_jpa.html
http://www.datanucleus.org/products/accessplatform/jdo_jpa_faq.html
http://www.datanucleus.org/products/accessplatform/persistence_api.html
It seems JPA is the "popular" choice backed by the big vendors (who love to screw you over if they can). It seems JDO is the more mature, seemingly superior choice which should enjoy more OSS community backing. (But does it?)
So what's a low-risk tolerance organization supposed to do? Is the difficulty of going from one to the other about the same? Has one started to emerge above the other at this point? Also, only because we currently use it, does Hibernate limit you to JPA-only? If so what is the most popular JDO implementation?