Great list! Very very well fleshed out, and full of nice references.
Here are some other references I could think of, but your list pretty much got the bulk of it.
- The orbs also call back to the blue laser scanning machine from the opening of Aliens.
- The closing monologue of Shaw echoes Ripley's closing monologue in Alien (and heard in Alien 3).
- Both the Prometheus and the Nostromo have their landings counted down (though the countdown in Alien was interrupted by the rough landing)
- The Weyland Corp logo combines elements of Alien's winged sun logo and Aliens's letters logo for the Weyland Yutani Corp.
- Finally, the last I can think of is how in the recent article, the colors of the Prometheus (a lot of black and yellows contrasting on the upper hull) are reminiscent of Chris Foss's bright color schemes for his Nostromo concepts. If you will, things like the ID numbers plastered on the hull are also on the Nostromo.
If I'm allowed to ask, what is the piece that plays in the beginning of Prometheus/Dallas listens to? I never realized they were one and the same! That's pretty cool.