Three very different games I actually took notes for :

La Mulana. In the "modern" version you have limited memory space to save some of the many texts you find, but you'll need more than that to solve the puzzles anyway. Good luck trying to scribble the weird pixelated symbols on your notes, too.

I play Shin Megami Tensei games with notes to optimize fusions, when I have a particular demon in mind and I want them to inherit the right skills. Later games let you see fusion results, but only one step ahead.

And then there's spacechem. I love Zachtronics games in general, and all the following ones tend to be progressive in difficulty and let you experiment from a good enough solution to better solutions. As the first, less refined one, spacechem is special. Before long it needs planning and calculations to even get something that works.