Oh, boy, that's a deep well to go down, especially if you're just now starting. Off the top of my head, here's some of my own personal favorites that aren't on your list:
Infinifactory & SpaceChem: My two favorite puzzle games ever. Infinifactory is a bit gentler in regards to difficulty, but they're both amazing and will completely change your expectations of puzzle games from now on. Basically, instead of completing the puzzle in the one way that the developer intended, you're given an input, an expected output, and a given area where you can make whatever solution you want. The challenge comes from making a solution that actually works and fits inside the given space.
The Binding of Isaac: Rebirth: Rebirth and its two expansions make up my most played game on Steam, with a little over 500 hours logged. The game functions like a basic twin-stick shooter, but with roguelike elements (permadeath, randomized runs).
Hotline Miami: A great top down shooter with some stealth elements. Amazing soundtrack.
VVVVVV: C64-styled platformer that's hard without being frustratingly impossible.
Braid: One of the first really big indie titles back when they started getting a lot of traction. Lots of really clever time-related puzzles. For example, there's a series of levels where time moves forward when you move to the right, but backwards when you go to the left. So enemies that you killed will come back to life when you move to the left, and so on.
Crypt of the Necrodancer: Rhythm-based dungeon crawler. Some of the randomized elements are weaker than something like Binding of Isaac, but still an amazing game.
One Finger Death Punch: It might look like those stickman kung fu animations that were all the rage in the late 90s, but there's a hell of an addictive game here. The entire game controls with just the two mouse buttons, but there's a surprising amount of skill required.
