I'm going to hijack and offer a specific example: Shivers. In addition to having puzzles with clues and inputs spread apart, it also offers a Flashback system that saves important pieces of information that you've already seen (Though actually taking notes is all but required since you still have to tab through the books then go back to the actual puzzle, and some clues are just images placed throughout the museum) The game just oozes atmosphere and tension with the changes in soundtrack and all the writing and environmental storytelling not directly related to puzzles. Once you know all the game's tricks, it does kind of take the edge out of the horror aspect, but even decades later it's still just a treat to walk through the museum's virtual exhibits.

Available on GOG right now, I suggest giving it a try, although do save your game often, as it's Win95 era.