Director's Cut is not good.
I haven't seen this film in years, but have watched the theatrical version many times. I love the film, but I think that might be an accident. The director seemed to have a vision for the story that he ultimately didn't get to flesh out properly. I think the theatrical version is so much better for it. It is a much better film with a little ambiguity and less-is-more approach.
I also noticed that the car scene at the end was really poorly done. It just looks very cheap and contrived to me now, I'm not sure if there were significant editing differences. It's a shame because it's the climax of the film. A lot of the special effects look quite dated now as well, like the thorax worm bubble things. I also thought some of the physics and philosophy was a tad shallow and pseudo-intellectual. One example I can remember is when Donnie was talking to his science teacher about travelling backward in time faster than the speed of light, and the science teacher just agrees that it is possible. I think most physicists would agree that time travel is only theoretically possible going forwards in time, and travelling faster than the speed of light is not possible at all.
Anyway, it's still a good film with a great atmosphere and killer soundtrack, and really excellent acting all round.