Stealing this from a thread on another forum, since it explained it quite well, and I don't see any point in trying to replicate its knowledge when I would just mess it up.
"It doesn't refer to the fact that you're 96% done with the game, nor does it mean that there's 96 levels in Super Mario World. The number 96 (or any other number at the end of your file) means that you've completed 96 goals. A few examples:
Star World 5 is one level, but has two goals. The regular goal completes Star Road and clears a path to the first Star Warp and Star World 1. The secret Goal advances you to the Special World.
Star World 1 is one level, but with one goal for getting the key and advancing Star Road, and a separate and distinct goal for completing the entire level, and advancing to nowhere. In the Game Boy Advance version, pressing Select while on the map screen will bring up level statistics, with all Star World levels showing two separate goals can be achieved. This takes a little bit more thought to figure out in the SNES version, as one would assume that you would need get each Star World level's keys to raise your score on your game file, since the regular goal gets you "nowhere".
Another pair of goals to note: The Forest Ghost House has two doors, one for advancing to Forest of Illusion 4, the other for getting a 3-up moon and building a path right back to Forest of Illusion 1. Both count as goals.
Therefore, a rating of 96 is equivalent to 100% in Super Mario World. I've never heard of 108 "percent", but I doubt it's possible. If anybody really has achieved any number equal to or greater than 97 on their game file, I'd love to know how."
