I thought we had a thread on this… Please post helpful answers, to help other readers decide if they might like your favs too. Of course, there are puzzles in many games in different genres. This thread is about games where puzzles are the main focus—so no Minecraft or Fortnite or similar...
Chip's challenge.
I didn't see it mentioned in the previous thread that was linked, but I remember playing this back in the day - a classic!
Even better (I just googled it), it looks like you can get it for free. There is a remake available on Steam for the grand price of $0.00.
I'm going to raise my suggestion of Infinifactory again (as usual).
Fancy building machines to create blocky products (a la minecraft), for your alien captors?
Then this is the game for you! A couple of the latter levels in particular have some macabre humour.