Zack Snyder announced at a press junket before the film wasz released about plans for Watchmen on DVD. It is as follows:
Summer/July: Director's Cut. This cut will feature "99% of what we shot," footage which Zack Snyder said he liked. The run time on this edition will be just over 3 hours long, compared to the 2:35ish run time of the theatrical version. It will be more violent, more sexy, and have more naked Dr. Manhattan. Also included will be entire scenes excised from the movie for time.
Fall/Last Quarter: The Black Freighter Edition. This title may not be the final title, but it is how Snyder identified it. He told us that they shot all the Ins and Outs of The Black Freighter pieces from the comic book, which for those of you who haven't read it, mostly revolve around a boy and newsstand salesman. You can see these characters in the film, but they don't have an impact on the story. The big news is that The Black Freighter, the animated movie, will be cut into the film. The animated film is said to be 22minutes long which, with the In and Out shots, will bump the presentation to about 3hours and 25minutes. Snyder referred to this release as the "fetishistic and kind of crazy" release, as it is so complete.
So, it looks like this director's cut available now is all of the live action film that will be available. But a later edition will insert this Black Freighter footage into the film.