Dummied Out: Scrap Brain Zone was considered to be included in, but was never finished, with only the collision and tile data making it into the final game. It uses glitched-out graphics from Final Zone, level-entry screen from the same stage and music from Star Light Zone. Oh, and it can't be accessed from the level selection menu at all.
There were supposed to be Chaos Emeralds at one point, except in the final release, the only thing that's left is the "You got the Chaos Emerald" jingle. And Robotnik juggling said Emeralds in the ending. It's not known, however, whether there was supposed to be any kind of code for this.
This game (and moreso its' hacks) is full of buried graphics - one of those, in particular, stands out in that there was a placeholder for the title screen called just "Mario". Then there's the Running Shoes monitor.
The "Somari Team Presents" screen was removed/replaced for obvious reasons, although the graphics for it can still be found in most hacks.
Green Hill Zone (and Marble Zone, depending on the hack) can only be accessed by level select in the Sonic hacks. More interesting, given that these versions of GHZ are actually edited to be a bit easier.
Special Stage is omitted in Doraemon, and can only be accessed by save state hacking. On the other hand, there is a new zone which occupies the Scrap Brain Zone slot.