It's a difficult one for me. I could not disagree with anybody who claimed that Super Mario World is the better platformer - it was groundbreaking, and every platformer since owes a huge amount to how much it moved the genre on. It took the strives made in Super Mario Bros. 3 (world map, non-linearity, etc.) and perfected the formula. I could go on about how much I love Super Mario World. And indeed, Yoshi's Island....w-w-w-WHAAT?! I really, proper enjoyed Sonic 3 & Knuckles, but tha what?! Each to their own of course, but no way whatsoever..... only Yoshi's Island challenges SMW for the 16bit platformer crown if you ask me (Zelda LttP taking the overall crown! )
SM3D World IS fantastic though!
Sonic 3 & Knuckles was special in very different ways. It was Sonic perfected - it is the closest thing to a flawless Sonic game, in my view. The broad array of terrains, the level designs, the way it managed to implement various different abilities without hindering the core Sonic mechanic (newer Sonic games could learn from this), and the genius musical score that maximised the hardware.
The main strength of Sonic 3 & Knuckles though? The non-linear level design. This is what sets it apart from previous Sonic games and all 2D Mario games. You don't just run from left to right, or up to down - the levels encourage you to explore the entire stage from left to right to left. There was so much to explore and you didn't merely 'run right' like 2D platformers traditionally did. In that sense, even the mighty Super Mario World comes up short.
That's why I cannot choose between them.