I’d have to go with either getting the Sheep Attack in Super Mario RPG, or finding Grate Guy’s casino in SMRPG. I had the player’s guide, thankfully, but how are you supposed to know that you get the Lamb’s Lure by using a Mystery Egg 10 times as Toadstool equipped with the B’tub Ring, then get Sheep Attack by using Lamb’s Lure 48 times? For the casino, you have to defeat a Chomp Chomp in a certain area and jump three times to make an invisible platform appear.
Lufia II’s ‘World’s Most Difficult Trick’ is up there too, which is a sliding block puzzle with 116 steps to complete.
And the goat puzzle from Broken Sword is so infamous it has its own Wikipedia page. https://en.wikipedia.org/wiki/The_Goat_Puzzle
The Witness has an insane puzzle on a sunken boat. Iirc you need to listen to some creaking metal sounds of the boat settling in combination with some other rules, including an invisible symmetrical line or whatever, it was kind of bonkers