Notch's natural eye color is brown, Herobrine's is silver, and Steve's is royal blue.

Surprising, huh?

Notch's black eyes are actually a result of extreme negative emotion or the presence of a Brine. If he were to suddenly grow angry, his eyes would darken to black. If a Brine were to be in close proximity, his body would react to darken his eyes to black. This is natural for him as it was originally added to his genetic makeup by Clotho so he would be able to tell when Herobrine was close by. If he uses a spell, he can keep his eyes as brown or black as long as he wishes. Notch is unable to change his eye color to any other color than black or brown, even with the aid of a spell or enchantment.

Herobrine's glowing white pupil-less eyes are also the result of extreme negative emotion. However, his eyes will also lighten to white when an Aetherian (spelled with, yet pronounced without, the er) is nearby. This was added by Atropos to warn him that Notch was growing closer. Like Notch, he can control the color of his eyes with a spell, though he cannot have an eye color other than his given silver or glowing white.

Steve doesn't have any special eye reactions.

Poor Steve, he's been left out.

Steve can change his eye color to a more natural shade of blue with the use of a spell.

The spells all three use to change their eye color is the same. It can only be used when the user is concentrating, so if one wishes to reveal their identity, they only need to startle them or distract them so that the user would lose concentration and drop the spell.

All the Minecraftian Council members know this spell, though not all use it.

Steve has the best control over this spell, then Herobrine, and finally Notch. Notch doesn't give a crap whether or not his eyes are black.

Steve often teases Herobrine that he is better at controlling his eye color than Herobrine himself. It gives Steve great joy to know that he is better at something than Herobrine.