His eyes are pitch black with two glowing red dots as irises and very small pupils. When he smiles, his mouth unnaturally widens and reveals yellow, fanged teeth (Sir JC explained that the yellow color is not due to tooth decay, but a side effect from when he was created). His fur is darker and he wears black and has either red or gray shoes.
Sonic.exe is almost identical to the original Sonic, but there are some noticeable differences.