That means that that version of the film isn't the theatrical version that the MPAA rated. So usually there is extra material that they wouldn't have been able to get into theaters with out an NC-17 rating. So most of the new material will be explicit, nudity, violence or language. It's not to be confused with a directors cut.
Basically, it means whatever wasn't in the theatrical version of the film and I know this because I've bought so many unrated versions of movies. Although, sometimes the DVDs contains both the theatrical and the unrated version and you choose whichever one you want.