Whenever I'm talking with game devs and we talk about a puzzle, my question is always: Adventure game, Myst, or 7th Guest. Mostly because I'm extremely old. But, in Adventure games, the puzzles were very much a part of the narrative. In 7th Guest, you just solved a classic puzzle. Myst was halfway.
Myst went a long way to contrive a world that was built of puzzles, so they were a part of the setting and story like a graphical adventure game, but they were so contrived, it felt closer to 7th Guest than Secret of Monkey Island or a King's Quest game.
For my part, I recently built a "click things in a certain order" puzzle to open a secret door. The things you clicked were next to tablets that basically had the code and implied the order. So I think it was more on the Myst side, almost to the graphical adventure side. I generally prefer those.
That's why I prefer Riven in that series. The puzzles can still be a bit obtuse and steeped in the logic of the game world, but with the game (mostly) raking place in one Age, it comes off a lot less contrived.
I'd tack on Carmen Sandiego. Broderbund managed to sell a ton of pocket encyclopedias that just happened to have a video game tutorial of how to use a pocket encyclopedia included.
