Thoughts:
Christmas tree scene was fine, just a small extension and more amusing Janek/Vickers material. Should've been kept in.
Fifield and Milburn finding the skin; aside from the fact that it's implied to be that of a Deacon breed, it's ultimately worthless. Felt like something that was never even in the shooting script but Ridley just decided to throw in to say "You know, there ARE other creature IN this movie". Lose it.
Shaw's speech was nice and fitting, but it should be cut right after the clash of the champagne(?) glasses, as the audio dip implies it was meant to be. The cut was placed there because Holloway comes it with rude drunkeness, which leads onto the next scene. This scene should be cut at the aforementioned moment.
The alternate version of Shaw and Holloway in their quarters was a good choice to swap out because it straight up made Holloway a drunken insensitive bastard. The scene in the theatrical release is much better as it keeps his intentions of a sweeter nature, having both of them make their cases on sober ground, and the sexual result is the same; and less forced feeling to boot. If the other version had been used, the intended impact when Holloway is killed would have been lessened. Lose it.
Vickers and David's comm chatter as she prepares to prevent the infection; a quick, badass scene for Vickers and more fun down talk from her to David. It felt like a spiteful queen ordering around her hyper competent subject, making it very cool. Makes me even wish, if it was in the movie, that David would have something to do with the death of Vickers in some indirect way... assuming she had to die. Definitely keep it.
Vickers talking to Weyland in an extended cut was mind-bogglingly better than what's in the theatrical cut. The scene had an actual emotional pull with it's newly added layer of dramatic tension between the two. Guy Pearce's performance is great and subtle, a portrait of denial, and Charlize Theron adds a lot of intensity to it when she begins to grill him on his choice, whereas in the theatrical cut she comes across as something of a pushover, and Weyland seems just seems like an utter bastard for the "Anything else" line. In the context of this alternate cut, she goes off on him, and he pushes her away, and in the theatrical cut it just comes across as cold. There is also a lack of dramatic music cue when she says "father" which makes it more bearable. Another thing is that the scene continues with Weyland sitting on the bed after Vickers exits... making the moment much more dramatically effective. One last thing that confuses me to no end is the fact that when Vickers puts her head down to Weyland's lap, the shot was originally cut on time with her movement, instead of awkwardly lingering on Weyland... unintentionally (I hope) imply oral sex. All in all, this scene kept extended is a must.