So as we find them, throw them up!
First thing is the ship that arrives at the start of the game, Haldin, is another Conrad reference. Haldin is a character from Under Western Eyes (https://en.wikipedia.org/wiki/Under_Western_Eyes_(novel) (https://en.wikipedia.org/wiki/Under_Western_Eyes_(novel)))
I'm guessing Yutani's second cousin is Jenny Yutani from the "Origins" novel. It's likely that she'd have taken over the company from her father. Also she'd probably be about 60ish in the 2130's.
On the 6th Level if you order Thorncroft to disconnect the cables in the reactor he will say "there have been unforseen consequences" wich clearly is a reference to Half-Life