If you want to see the power of editing (and the power of moving your notecards around while writing), the Criterion version of 'Brazil' with the infamous 'Love Conquers All' cut is a brilliant example of how an editor can literally (I mean that literally) create a new story out of the same basic elements as another film.

McCabe and Mrs. Miller has a version with interviews with Robert Altman and Producer David Foster. Great insights from both.

Both Ridley Scott and Danny Boyle tend to do pretty comprehensive director's commentaries for their films. The best of these is Alien (Scott) and 28 Days Later & Sunshine (Boyle). On the blu-ray release of "Night of the Hunter" is 'Charles Laughton Directs', a 2&1/2 hour documentary on the making of the film including deleted scenes and his specific direction for parts of the movie, it's pretty great. As mentioned in the lists above, the Lord of the Rings Trilogy extended versions have an amazing set of production features.

I have a soft spot for The Criterion Collection. They have wonderful commentaries and documentaries. Unlike some of the extras on blockbuster films, they are not made for publicity reasons, but try to go much further, offering in depth information about the films. - Brazil, as @Matthew Rigdon mentioned. - 8 1/2 - conversation with Vittorio Storaro about Gianni di Venanzo - Ingmar Bergman Makes a Movie - Writing for Truffaut on The Antoine Doinel box set - Peter Bogdanovich talking about Lubitsch's Trouble in Paradise - Traffic's commentaries - Soderbergh, another with the producers. - Tokyo Story's commentary - Silence of the Lamb's commentary. - Seven Samurai's commentary - Robocop's commentary - Paul Verhoeven - Red Beard - commentary by Stephen Prince - Rashomon - commentary by Donald Richie - Peeping Tom - The Passion of Joan of Arc commentary - Fassbinder's BDR trilogy - Eisenstein's Visual Vocabulary - Ivan the Terrible - "It is wonderful to create", "A message from Kurosawa: for beautiful movies" and Stephen Prince's commentary on Kurosawa's Ikiru On the non-Criterion front: - Citizen Kane has two wonderful commentaries, one by the late Roger Ebert, another by Peter Bogdanovich. - Fight Club's commentaries (4) - Toy Story Box shows how it was made, from inception to release. - Obsessed with Vertigo and a commentary by Robert Harris on Hitchcock's Vertigo - "Within a Minute: The Making of Episode III." on Star Wars Episode III - Scorsese on Scorsese on The Departed, 2 DVD edition - The making of Psycho, commentary by Stephen Rebello - Psycho - King Kong - Production diaries (Peter Jackson) - Commentary by Guillermo del Toro on Hellboy - Coppola's commentary, extras on The Godfather trilogy - "Fear of God" documentary and Friedkin's commentary on The Exorcist (NOT the commentary on the director's cut). - Die Hard, the five star platinum edition. Especialy the text commentary and the commentary. - Blade Runner - commentaries, a lot of extras.