I think the EE are definetely the versions that PJ had in mind when he started making the LOTR movie. And I think that when one is discussing the movie or its values he must refer to the EE versions. There are some parts cut in the theatre versions that make the movie more vital and ,for someone who hasn't read the book, give much more reason and explanations about what is going on the screen.
I am impatiently waiting for the ROTK EE :).

What I do regret is that the magic thirst of expecting every part of this beautiful trilogy will soon be sated...