In Chapter 3 (The Consequences DLC), there's a soda vending machine with a brand named "BRAIN". By interacting with it 15 times, a painting on the corner of the wall will fall to reveal a peephole. If you interact with it, you'll see a hidden room with a Shade dancing for three Haunted wielding glowsticks. The Shade will eventually notice your presence.
Contributed by ProtoSnake
The music that plays in the save rooms is a rendition of Claude Debussy's "Clair de Lune".
Contributed by Kitsune Hawk
In chapter 6, Spoiler:saving Joseph's life from hanging on the bridge will award the trophy / achievement "Everybody Gets One".

This is most likely a reference to Family Guy, in "Let's Go to the Hop" and "Believe It or Not, Joe's Walking on Air" when Spider-Man says it to Peter Griffin and Cleveland Brown after saving them from a fall.
Contributed by ProtoSnake
After the player gets out the crash site, they'll find Connelly who is eating a dead body. This is a reference to the original Resident Evil, specifically the player's first encounter with a zombie who is eating Kenneth. Shinji Mikami was the director of both titles.
Contributed by ProtoSnake
The game's working title was "Zwei", the German word for "two". This was in reference to the game's original premise of two vampire hunters attached to each other by a chain.
Contributed by Mass Distraction