I now have both the 1997 Director's cut DVD which I bought about 10 years ago and the 2004 uncut version DVD which I just purchased.
Technically, the director's cut is better. The sound mix which was remade for that DVD has a deeper, more robust sound, especially the underwater noises (i.e. sub creaking, depth charges, breaking up noises). The sound mix in the uncut version is from the TV mini-series and it shows. You wont necessarily notice the difference on a TV, but on a Home Theater system like I have, it is night and day.
In terms of image quality, it is about the same, although I find the image quality on the Director's cut is slightly sharper. On the Uncut version, the image, especially on the newly added scenes is a bit fuzzier.
Having said all that, the uncut version works better as a movie, since the new scenes fill in and complete the movie and tie it in more to Buckheim's original book.
so get both....