I really liked the misanthropic mindset of the devs. Look at Mothership Zeta: The place was very neat and tidy, but as soon as the humans set up their camp in engineering, it becomes dirty, cluttered with junk and messy.
Also, I am really fond of how they arranged teddy bears every once in a while. Be it a skeleton of someone who apparently shot himself while holding a teddy bear, be it the two busy teddy bears that I found in some factory once (I don't recall where that was, but they definitely had fun), be it the teddy bears of Jericho. The bears really add some character to the game.