As they’ve already been mentioned before, I will second both La-Mulana (and though not mentioned, it’s sequel), and FEZ.
The Witness didn’t make me break out Pen and Paper, but it was definitely one I had to give my brain a break and come back to to look at things from a fresh angle.
Now for some previously unmentioned finds where your attention to detail will be rewarded. Not all will require notebooks. But there puzzles hidden in all of them.