This box set of the TOS movies:
has the theatrical cuts of 1, 2 and 6. The 2 disc SE's have the director's cuts of 1, 2 and 6. All the other movies (TOS and TNG) are the same cuts in either set.
This box set I linked too is actually the first time the theatrical cut of The Undiscovered Country has been presented on home video, and the first time the movie has been available in it's original 2.35:1 aspect ratio (instead of being opened up to 2.00:1).
(sidebar, I also did a little hack to this box where I replaced the bonus disc case with a 2 disc case and put my DVD copy of the 2009 movie in there since I also had it on Bluray).