Here's some I noticed, and a few are ones I saw when I googled the two.
I instantly thought of The Shining when we see the carpet with a repetitive pattern in a narrow hallway.
The bathrooms at the studio and the red bathroom from The Shining have a similar aesthetic.
This might be a reach but with all the other Shining references I don't think so.
I didn't think of this watching the movie, but it makes perfect sense that Sue is the young lady in room 237 and Elisabeth is the old lady. I caught the nods that Elisabeth was turning into an old witch or "Crone".
Here's a good collage of gifts from The Shining and The Substance.
I didn't get this one either. I haven't seen 2001 in a long time but looking at them its obvious.
Some other horror movies
Re-Animator
This blog has good examples. There's more but I picked the 2 that I thought of when I saw the Substance.
THE SUBSTANCE
The Fly
From Beyond
I think the star earings that sue wears is a reference to Coralie Fargeart's rape revenge movie, Revenge.
Revenge has a bunch of gratuitous butt shots in the movie like The Substance. Demi Moore is the model from the I Spit on Your Grave Poster