I really enjoyed The Witness. It has exactly that sense of discovery and building on previous knowledge by making leaps that feel like your own - not leading you by the nose, but not leaving you lost either. A credible attempt at worldbuilding and the lovely environment really helped too.
As with all such games, watching solutions and playthroughs completely destroys the experience.
Desktop Dungeons was fun, albeit a bit too rooted in simple, but somewhat laborious, math. Works because it’s random, there are so many solutions, and it’s not too hard to find one. Very different genre to the Witness.
SpaceChem was another favourite of mine, but it got hard about 3/4 of the way through, life intervened, and now I have no way back in. I’ve lost the skills I learned, and re-learning them by re-playing all(?) the intervening levels doesn’t appeal. Again, I’d say that this feels like a very different type of game again to The Witness and Desktop Dungeons, in that is has crafted puzzles, like the Witness, but allows “bad” and “better” solutions and the freedom to make them, like Desktop Dungeons.
I’m sure Zachtronics subsequent games are just as good, but I seem to need a specific set of circumstances to really get into a puzzle game, and I can’t see myself having the time and clarity necessary for the forseeable future.