Well, I have 95, and am still one short. So, I'll throw off a few you should find.
First, you surely beat "Funky" in the Special world, right? The wrld will now be Autumn.
How about the "Top Secret Area"?
Or the water level below the "Cheese Bridge"? That one leads to the star road.
There's also two levels in Chocolate Island that have secret paths. One leads to a pipe which contains an underground secret world. The other loops around in a circle leading back to the same level.
Oh, I am also guessing that you have to beat Bowser through both the Front AND the Back door. I have. I think they count as two levels.
Also, the level under the "Bowser Star Entrance" leads to the star. Get that one too.
Make sure you got both exits in all red levels. Which I am guessing you already checked.
I am really stuck on the 96th one. So when you find your 95th one, tell me! We're prolly missing the same level.
___________________________________
I will not rest until Mario and Luigi get a REAL 3d Mario Bros. Game.