Super Mario Galaxy for me. Super Mario 64 is great and still fun to play, but in terms of better 3D platforming, Galaxy takes the cake. The look, the new gameplay mechanics like gravity, the controls, the music, the difficulty, everything was well done in both Super Mario Galaxy games. So far if you want the best of what Mario has to offer play the 3D games. 2D ones are great too, but I feel like with the 3D games Nintendo tries to reinvent Mario, as opposed to perfecting the fundamentals like they do with new 2D entries.
I've never been as impressed with Super Mario Bros. 3 as most other people have, even when I was a kid. Super Mario World is great, probably my favorite 2D Mario, but it still does not impress me as much as say Super Mario 64, or Super Mario Sunshine.
Edit: Honorable mention to the first two Paper Mario games. Even though I count Mario RPGs as their own deal, these two games are phenomenal to say the least. Filled with interesting little stories, awesome characters, lots of fun stuff to do. Great experiences all around.