Very often someone ask me what to use for persistence in modern JEE applications: JPA or JDO? Well, JPA is born after JDO and seems to be official supported by Sun since it's part of EJB 3 specification.
But my response is always the same: use a JDO implementation if you want a more powerful tool. JDO 2.1 is a superset of JPA 1 standard.
A feature matrix is available here: http://db.apache.org/jdo/jdo_v_jpa.html