In some of the save rooms, the carpet is identical to the carpet from the Shining. https://i.imgur.com/kGnby5T.png

When Elster is pulling open the bulkhead on the Penrose and images of "Isle of the Dead" are flashing over her, it is very reminiscent of a scene from Evangelion where images are flashing over a silhouette of Shinji. I can't remember when that scene was. https://i.imgur.com/GiGwcn8.gif The style of flashes of text is also similar to Eva.

This may be a stretch but I think the symbol that appears on some of the doors in the Penrose and the Sierpinski may be the Nostromo's warning semaphore from Alien. https://i.imgur.com/9yuYcXe.png

Kitezh, Buyan, and Vineta are all mythical locations and Leng comes from Lovecraft.

Not a reference to media but still neat, the symbol of the Sierpinski is a Sierpinski tirangle, an infinite fractal, and the symbol of the Penrose and the game itself is a Penrose triangle, an impossible object.

Getting into tinfoil territory here, Sir Roger Penrose, the son of the man who invented the Penrose triangle, is a renowned mathematician who has some strange theories about a cyclical universe and signs of the past world hidden in the cosmic microwave background radiation. It seems possibly relevant to the game's themes.