Lars, At the moment, I would think 2.1 is most used. If not that, than 2.0. However, this will be changing as time goes on. As we learned in last week's book promo, WebLogic is coming out with their EJB 3.0 compliant server soon. (It's currently only JBoss that has EJB 3.0 out.) This lack of vendor support is currently preventing people from using 3.0 in production.
While 3.0 is easier to learn, it is important to be familiar with the underlying concepts. It's not that it is most used. It is that you are more likely to find a project converting 2.1 to 3.0 than starting a green field project with 3.0.