GMTK has done some videos on this, and does great observations on the gameplay designs of some games.
- How Nintendo solved Zelda's open world problem
- Designing Difficulty in his magnet themed puzzle game
For me, a good puzzle is when the concept is introduced to me bit by bit, then extended from there. Unfortunately this can be a bit of a fine balance as some game will literally dedicate too many levels for each new concept, and so the puzzles bore out easily.
In other news, I've really been enjoying Paquerette Down the Bunburrows. Don't mind the "( ≧∀≦) I luv bunnies <3 <3" theme, the puzzles are neat and gets progressively harder, and has nice collectibles and secrets that greatly extends the gameplay.