Phobos was cool. A nice little bit of bonus character development. I like to think the sounds and images of the aliens weren't actually part of the test, more like prophetic associations for the audience.
I just watched the extended/deleted scenes. I'm kind of insulted by most of them. Cutting a line or two of dialogue isn't worth a special feature. The only scene I wish had been left in is Crossing the Plaza, but even that wasn't terribly important.