Well it all depends on few questions :-
1) is your project is using any
EJB ?..Then go for that version
2) If there is no ejb in project and you are doing this for your own learning, then i would recommend go for EJB3.0 as that's new and latest.It's always good to read latest.
But if your project is using EJB2.0 and you decide to go for EJB3.0, then make sure you dont get confuse between two version.
[ March 07, 2007: Message edited by: deepak adlakha ]