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