Not sure if they really count as a puzzle game.
but I enjoyed the following HOPA's that have puzzle elements.

Drawn: Dark Flight
Drawn: Painted Tower
haven't tried the 3rd one yep

Bookworm.

not interested in the GA but my favorite puzzle(ish) games would have to be the magic circle or pony island if they count...if its pure puzzle than idk I like those logic puzzles where you have to fill in the cells that look kinda like this

View attached image.

Thank you!

Right now I'm playing infinifactory.

Hexcells

I would say Antichamber, I find that game amazing.

I love the Tetris Attack/Panel de Pon/Puzzle League-style games a lot. My favorite is probably Pokemon Puzzle League, because of all of the features and content. But even the super bare-bones version you can unlock as a minigame in Animal Crossing: New Leaf is damn satisfying to play.

La Mulana if you want to count it as a puzzle game. I certainly do. There's some standard metroidvania gameplay, but the reason people take 40+ hours to complete the game is the difficulty of the puzzles.

Chess I guess.

Hexcells is the besht.

Hard to say... The first 3 Myst games, Adam Wolfe (if you count that as a puzzle game), but in general any kind of brain teasers would be among my favorite (Hercules for example, as previously mentioned in these posts)

Thanks for the giveaway.

INFRA - Puzzles, actual scenario, perfect graphics, logical level-design and a very good story.
For me the true game of the year 2016/2017.

Second best is The Talos Principle. Before INFRA was released, this was for me the very best puzzle game.

hyperrogue

Pandora's Box

Thank you very much for the awesome-looking puzzle game!