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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?

A: 

@Crusader - what makes you think that anyone on SO has a better crystal ball than you do?

So what's a low-risk tolerance organization supposed to do?

Pick the alternative that it determines to be the low risk solution. How it determines what solution has the least risk is ... unclear ... but I don't think that asking SO is a valid risk assessment procedure.

The other point is that choosing JDO when JPA is the "winner" (or vice versa) probably won't kill your project in the short or long term. The consequences of making the wrong choice are most likely limited to greater staff training costs, and being stuck with base ORM platform where development has stagnated and support is increasingly expensive. [I'd protect myself against the latter by picking an open source ORM platform ... either way.]

Is the difficulty of going from one to the other about the same?

Probably yes. Especially when you consider data migration issues.

Has one started to emerge above the other at this point?

JPA seems to dominate these days. The JDO folks would say that their way is technically superior, but that's not the point.

Also, only because we currently use it, does Hibernate limit you to JPA-only?

JPA plus Hibernate-specific extensions. Certainly Hibernate does nor support JDO and it probably never could.

If so what is the most popular JDO implementation?

Pass.

Stephen C
"better crystal ball" - Just interested in popular opinion. You're right but I feel it's important to gather second opinions as a part of the decision making process.
Crusader
development stagnated ? on which ? JPA or JDO ? seems like both are progressing along nicely with major releases recently. Similarly with their implementations.
@user383680 - I'm talking about LONG TERM risks.
Stephen C