A) A version that was simply too long for theaters (IE Dances With Wolves)
B) A version that had too much violence/sex to be considered for R (IE American Pie movies)
Filmmakers don't like to give their movies an NC-17 rating. It basically cuts down on a huge amount of profits.
Some films that have been released as NC-17 (or it's older rating, X) are Midnight Cowboy (which was re-rated to R) and A Clockwork Orange (also re-rated an R).