Yoshi's Island. Nothing else comes close. SMB3 and World had some great ideas, but the levels are ultimately too short, and the presence of time limits only discourages exploration. There are a lot of fine details about YI that I like as well: an in-level inventory, a scoring system that isn't arbitrary, a map system that doesn't involve tedious manual backtracking like SMW... It's just a way more polished game overall.