Fairune 2 and Submachine: Legacy were the last two where I needed to take notes.
For Submachine, I was mainly writing down coordinates of locations where I figured I could come back to use an item later, or information from signs that might be useful in a later puzzle.
For Fairune, I had to make multiple maps on graph paper to keep track of all of the things I wasn’t sure how to solve or needed to come back to with new items.
I have also been writing down some numbers for System Shock, but I haven’t finished that one yet, and I’m not sure if the note taking will need to be any more extensive.
The Talos Principle. After a short bit in the game, you go to a hub area that goes to other areas like the one you just came from. Eventually, you find out that there is another hub area above this which leads to other hub areas. I didn’t remember if there is another layer on top of that, but either way, once I hit that second hub layer, I remember realizing that the entire game was multiple times larger than I had thought, and I had no way to know if it would expand again when I made it to the next area.