One of the first pieces of advice Amma gives to Ethan is that "the eyes are the windows to the soul" (9.02.37). Boy was she right. Although we don't know what that says about Mrs. English and her one glass eye.
Lena is different than any girl who's ever set foot in Gatlin, and she has the eyes to prove it. Ethan says she has eyes "so green they could've been considered some new color altogether" (9.02.62). They're also deep and endless—maybe even a portal to another world. They might as well be, since Lena's Caster powers aren't exactly mundane.
Another character with telling eyes is Macon Ravenwood. His eyes "were clouded over, tinted, like the glass of the hearse windows" (9.14.189). Hmm, opaque and mysterious, just like Macon himself.
Not everybody has gorgeous green eyes like tropical tide pools. Some of Lena's relatives have eyes that are more human than animal. Genevieve (of Civil War flashback fame) has eyes that change to gold when she uses The Book of Moons to resurrect her Ethan. From that, we can conclude that gold snake eyes are, um, not a good thing. Remember Michael Jackson at the end of "Thriller"?
There are even variations on creepy gold eyes. Genevieve, Ridley, Sarafine, and Larkin all have them, but Larkin's are always described as a snake's. Maybe that's because he can morph his body parts into snakes (although so far we've only seen him do it above the waist, thank you very much). Once again, the eyes are more revealing than you might think.
We're not sure what the green of Lena's eyes symbolize (youth? naivety? greed? envy?), but by the end of the book she's only got one of them. Don't worry, she still has her depth perception—it's just that her other eye has gone gold. As far as we know, her newfound gold eye doesn't have a nefarious-looking slit in it, which is a step in the Light direction for Lena. But her eyes do show that something has changed inside her.
One of Lena's poems reveals her struggle to come to terms with her new eyes: "First green is gold but nothing green can stay" (12.13.34), she writes. She's taking inspiration from Robert Frost (or The Outsiders to which we can say, stay green, Lena!) but switching it up a bit.
Maybe in this world, green is innocence and gold is evil. It wouldn't be a stretch to say that Lena has lost her innocence by the end of the book. After all, her mother has tried to kill her, her favorite relative is dead, and she almost lost the boy she loves. She's lucky she doesn't have a premature gray streak in her raven-black hair.