The only version of Alien that I own is the 2003 dvd with the theatrical and director's cuts branched together. It's only been two years since I first saw the film, and I tracked down a copy of that dvd specifically so that I could see both versions (most stores around here were only carrying the old release), though of course I viewed the theatrical cut first.
Consequently, I'm only familiar with its colour timing from that version. I had a look at the screenshots on dvdbeaver that were linked to earlier, and it seems to me that there isn't really that much difference, at least not how I'd imagined from reading this thread. The older transfers from the 90's are kind of flat and washed out, the pal version being too green and the first ntsc too red. The '03 has better contrast than either, though in some shots the whites are a bit too hot. The Bluray timing looks the best in many shots, though it has more blue than any other version, which is occasionally a bit too much. In general it resembles the '03, with some differences, which to my mind is a good thing.
But these aren't huge differences we're talking about here. When I started reading this thread I was having visions of 2004 Star Wars type of changes in colour, but it's not even close to that. The colours as presented in the newer transfers still look like images that were actually photographed and haven't been excessively tampered with as some seem to think.
I don't yet have an HD display, so I have to stick with dvd for the time being, but I'm not worried about the colour issues for Alien after seeing those screenshots. A while back I made my own version of an isolated score from the Intrada cd release and synched it to the theatrical cut, so I don't even need to get another version for that. It seems to me that in making the so-called "director's cut" there was a huge missed opportunity in that they could have gone back to the score as composed by Jerry Goldsmith--now that would have made for a worthwhile alternate version of the movie! With just a bit of trimming here and there it works remarkably well, and in nearly every case what he composed suits the film far better than the hacked up mess that they actually used. Of all the misguided and foolish things that have been done to movies, that has to rank as one of the worst.