Surprised nobody mentioned Fish Fillets 2, which is a top 3 puzzle game imho.

My list:

    1. Antichamber
    2. Fish Fillets 2
    3. Baba is You
    4. Ittle Dew (esp. the Master Dungeon)
    5. An Architect's Adventure
    6. Cosmic Express
    7. Talos Principle
    8. Stephen's Sausage Roll
    9. Portal
    10. Cocoon

Fish Fillets 2 looks simple, but it's one of the toughest puzzle games out there. Especially getting the stars on each level. I love it because the rules are simple, everything's there on one screen, but figuring it out requires a lot of out of the box thinking.