Prakas,
It really depends upon your need. Ask yourself a few questions before you go in any particular direction.
How big is your app going to be, and how big will it ever possibly be?
If it is small and guaranteed to stay small (be careful about answering yes to that, though!) then any proprietary persistence framework, like Hibernate, could serve your need. If you ever need to change for politiacl reasons then it won't be too big a deal.
Are standards important to your company? If so, then you will obviously want to make a descision that won't gt you in trouble.
When is your app slated for completion? JDO 2 could be final by the end of the year and EJB 3 will be final in first quarter of next year, so if you will be complete sometime in the next year then
you should be safe either way.
How much risk are you willing to take? JDO does not have any support for any of the major vendors, but the spec seems to be headed in the direction of open source, so if you are comfortable with it there then it could work for you.
EJB 3 is the endorsed spec for the new
Java EE platform, and has the support of all of the vendors, but only Oracle and
JBoss of the major Java EE container vendors have preview implementations to date. If you are looking to use WebSphere, for example, you might want a release from IBM, and it could be a risk if it is not ready when you need it.
Hope this helps,
-Mike