In Dead City there's a Bistro called "Mama Dona" - obvious reference to Miss Donna, the ID mom.
The Doom room has "e1m1" scratched on the left of the door frame.
Lots of references to Mixom throughout various locations, who - as we all know - are the company who accidentally delivered chainsaws instead of jackhammers to a certain Mars base.
The caves leading to the old distillery have "GLO-REE-UHH" and a picture of a flower scratched into a rock - no idea what that refers to, but is obviously a personal message from an artist.