8-bit Link’s Creepy Eyes Finally Explained
Digital Unrest, a delightful video game based webcomic, has come up with a few theories on his green/brown eye holes.
It seems that the theories range from green eyes with chronic fatigue to brown eyes with green eyeshadow and a few more exotic ideas.
Link's apparently also part of the Knights Templar.
The story goes that you can only put so many colors per character so they found many ways to repeat colors on characters to fit within that capability.