Oh, there are more. Out of my mind, I can cite The Talos Principle, Qube and Antichamber.
Maybe in slightly different categories: Fez (~2D), Mirror's edge (parkour), infinifactory. The Stanley Parable as well, perhaps?
Then there are numerous 2D ones, and I'm pretty sure I am forgetting some that I have in my library. Portal isn't unique, but it has one of the most dynamic and entertaining narratives. It also spearheaded a whole lot of "portal clones", which was nice to see, as I quite like those puzzle games.
From your first three I've only seen Antichamber. I agree that it's a cognitive challenge like portal, but I also think it doesn't involve the same kind of spatial reasoning portal does. Well, at least not in the (otherwise ubiquitous) 3D space.
Well, the most difficult part of Antichamber is that the 3D space is a non-euclidian one, so you have to adjust the way you think space. But I still think that the main game element is how to find your way from point A to point B in that space. And pathfinding isn't a trivial exercise in euclidian space, already, which is the point of the article.
I recommend the Talos Principle, even though I haven't finished it yet. Some challenges are quite hard, and it has even more spatial reasoning than portal. Here also, enigmas revolve around getting you from point A to point B, but you usually have to carry along some tools to help you. This often ends up being a variant of the Hanoi tower, or the wolf, goat and cabbage, but in a space with more than one dimension, unlike those classic riddles. And there is some lore hidden in the game world that can be quite interesting to puzzle together.
Now, if you want more portal, the game modding community is quite profusive around Valve's IP. You have Portal stories: Mel, Aperture tag, Portal: prelude. The quality is often worse than complete games, but the puzzles can be quite challenging.
I haven't played Portal, but, based on what I've seen of Portal, Human Fall Flat may be similar. You solve puzzles in a 3d world to get through stages of the game. It's pretty fun.
