I purchased the iTunes version last night, and it does in fact come with all of the special features on the blu-ray. I agree with Necrotard that both Advent and Phobos were really good. Advent gives us some more information about David and Shaw, David's motivation, and some details about his genetic experimentation. It seems that Advent is supposed to be part of David's transmission to Weyland-Yutani at the end of the film, just a longer version of it with lots of recording from his lab. I need to watch it a few more times to pick up on all of the nuances, but you basically get to see David at work, which is pretty fascinating. It also helps set up Ridley's desire to move into Alien. It more or less establishes WY's awareness of a dangerous alien lifeform, which ties in directly to Ash being aware of it as well.
Phobos was an interesting character development piece that was really enjoyable, but obviously something that could not have fit within the context of the film.
Overall, the deleted and extended scenes were underwhelming. I do wish the extended plaza scene had been left in the film as it makes the civilization seem grander, more mysterious. I thought that the scene in Daniel's apartment, though brief, would have been a nice addition as it introduces Branson and shows us their love for one another. It would have made his death a little more meaningful.
And, in my opinion, the extended funeral scene gives us a few seconds of conversation between Daniel's and Walter. I actually think this should have been left in as it helps establish further the relationship between those two. There are a couple of moments of them connecting that were cut. Keeping at least one of them in the film would have made David's comments about Walter loving Daniels seem more insightful.
