This is an old theory, and not as relevant as it used to be, but potentially may still be important. This is still going to be lengthy, so please bear with me.
(1) Bast says that humans can tell Fae by their hair and eyes.
- “Second secret,” Bast said. “The fae folk look nearly like we do, but not exactly. Most have something about them that makes them different. Their eyes. Their ears. The color of their hair or skin. Sometimes they’re taller than normal, or shorter, or stronger, or more beautiful.” – The Lightning Tree
(2) The only people, aside from Kvothe, in the entire stories whose eyes change color are Fae - Bast and Felurian.
- “As he spoke, Bast’s eyes grew paler, until they were the pure blue of a clear noontime sky. [...] Bast’s eyes were now the pale blue-white of lightning, his voice tight and fierce. [...] Bast leaned closer until their faces were mere inches apart, his eyes gone white as opal, white as a full-bellied moon. [...] His eyes were a human blue again, his smile warm and charming.” – The Name of the Wind
- “Felurian slowly relaxed out of her stretch and looked at me with ancient eyes. Eyes unlike anything I had ever seen. They were a striking color... The summer dusk was in her eyes … a sort of twilight blue. [...] Flashing moon silver, midnight blue her eyes [...] Her eyes were of the bluest black / 'Like night sky with the clouds blown back [...] I handed her a violet, its color dark as her eyes. [...] She didn’t look away from me as she spoke. And though I hadn’t looked away or seen them change, her eyes were no longer soft with adoration. They were dark as storm clouds, hard as ice.” – The Wise Man's Fear
(3) ... oh, and also Kvothe:
- “Speaking of. Did you know that when you’re angry your eyes—” [...] “I thought I was imagining it before,” Denna said, looking up at me. “But your eyes really do change color. Normally they’re bright green with a ring of gold around the inside….” [...] “But I’ve been watching. When you broke the pump handle yesterday they went dull green, muddy. And when the swineherd made that comment about the Ruh they went dark for just a moment. I thought it was just the light, but now I can see it’s not.” [...] “People probably are distracted by your hair. It’s so bright. It’s pretty…. pretty distracting. And your face is really expressive. You’re always in control of it, even the way your eyes behave. But not the color.” She gave a faint smile. “They’re pale now. Like green frost. You must be terribly afraid.” – The Name of the Wind
- “Stop. Just stop,” Wilem said, startling both of us out of our argument. He turned to Mola. “When Kvothe came here unconscious, what did you do first?”
- “I checked his pupils for signs of head trauma,” Mola said automatically. “What the hell does that have to do with anything?”
- Wilem gestured in my direction. “Look at his eyes now.”
- Mola looked at me. “They’re dark,” she said, sounding surprised. “Dark green. Like a pine bough.”
- Wil continued. “Don’t argue with him when his eyes go dark like that. No good comes of it.”
- “It’s like the noise a rattlesnake makes,” Sim said.
- “More like hackles on a dog,” Wilem corrected. “It shows when he’s ready to bite.”” – The Wise Man's Fear
(4) If Kvothe is Fae, I believe this is from his mother's family line.
- "Denna said, looking up at me. “But your eyes really do change color. Normally they’re bright green with a ring of gold around the inside….”
- “I got them from my mother,” I said." – The Name of the Wind
- “My father was looking down at my mother, nestled under his arm. “How about it, woman? Did you happen to bed down with some wandering God a dozen years ago? That might solve our little mystery.”
- She swatted at him playfully, and a thoughtful look crossed her face. “Come to think of it, there was a night, about a dozen years ago, a man came to me. He bound me with kisses and cords of chorded song. He robbed me of my virtue and stole me away.” She paused, “But he didn’t have red hair. Couldn’t be him.”
- She smiled wickedly at my father, who appeared a little embarrassed. Then she kissed him. He kissed her back.
- That’s how I like to remember them today. I snuck away with thoughts of the University dancing in my head.” – The Name of the Wind