Chao Garden - Early versions of the Chao Garden...
Chaos 2 - Room looks darker and is empty.
Chaos 0 - Cop cars are in different positions.
Chaos Battle (hi res)
And what the hell is this helicopter doing here?
Casinopolis - different shower and Sonic isn't performing the proper animation.
Casinopolis - Cowgirl isn't in the final.
Emerald Coast - Sonic's doing his pose in the middle of the level.
Emerald Coast - Different camera angle.
Emerald Coast - No speed boosts on the bridge with the whale chase scene.
Egg Carrier - Hedgehog Hammer's menu is different.
Egg Carrier - Tails is jumping onto his unharmed plane which normally crashes onto the Egg Carrier.
Egg Carrier - The E-Series robots with similar textures.
Egg Carrier - Eggman and Sonic confront with a different camera angle.
Egg Carrier - Big in a slightly different looking Egg Carrier interior.
Egg Carrier - Knuckles also inside a different looking interior (high res)
Egg Carrier - Sonic in a different looking "captain's room."
Final Egg - Amy is being chased by Zero in a hazard-less Final Egg.
Hot Shelter - Amy doing her character select animation in the level.
Ice Cap - Sonic standing on a different panel.
Sonic trickboarding in Icecap (anigif)
Ice Cap - Sonic doing tricks not present in the final.
Ice Cap - Tails in an unfamiliar part of Ice Cap with lots of trees obstructing the path.
Ice Cap - Sonic walking on a bridge that can't be accessed in the final...
Lost World - Slightly different looking Lost World.
Lost World - These fire arrows aren't here in the final.
CG Movies - This Chaos Emerald scene doesn't play in the final.
CG Movies - Neither does this scene with the exception of it making a slight appearance at the end of the intro movie.