Favorite "puzzle" in any game ever
This happened about two years ago but I thought of it recently. I had just fallen through the Brittle Hollow black hole yet again and the supernova music started playing, so I decided to aimlessly drift off into space. Then I saw the Tower of Quantum Knowledge that I had been spending days trying to get into just floating around in space. I hadn't even considered "I have to let it fall through the black hole" as a solution to how to get in.
Unfortunately I had already completed the Quantum Moon, so I didn't really learn anything from getting in, but I loved how you "discover" the solution after failing (and falling)