I have a feeling we've had a poll like this before, but I'm too lazy at the moment to do a search. :P
Anyway, it's an easy choice for me: SMB3. I didn't play SMW through for the first time until a few years ago, and while some may argue nostalgia is making my choice, I don't think so because I constantly play older games that are new to me and I have no problem falling in love with them and even ranking them above childhood games. The real reason SMW doesn't come close is most of all the fact that it's so dang easy. Really, not much about the game has stuck with me, and I blame the fact that I blew through it like nothing, even getting all 96 exits. Even the so-called "difficult" secret world stages barely presented a challenge. SMB3 puts up a healthy challenge in many parts, especially if you play the Japanese version. Unlike SMW, I can still picture most of its stages in my head, and they're also so inventive too, more so than SMW I'd say. Some things stylistically about SMW don't sit right with me either. Like the football-themed enemies are just odd and feel out of place. Never really cared much about Yoshi either or the physics of cape-flying.
Don't get me wrong, Super Mario World is a fantastic game, but it doesn't come close to outshining SMB3.