Windows of the Soul

Traditionally, the eyes are the windows to the soul. Thus, when we see a subtle emotion in someone's face, we say that we see it in his eyes.

It doesn't matter if we can really do this. We do read emotions off people's faces, in such fantastically subtle and sensitive ways that we're often not consciously aware of them. So, wherever it really is that gives them away, we say and often believe it's in the eyes.

On occasion, the things that we're told can be seen in someone's eyes can get really subtle or really abstract - from sadness or murderous fury all the way to humanity or immense age.

This is a trope of literature and dialogue. You need this sort of description only if you can't see the person's eyes for yourself. Live-action works generally let you interpret for yourself; drawn works will often depict the emotions graphically.

Often a contributing factor to Uncanny Valley - viewers will say there's "something wrong with their eyes", and creators that they "can't get the eyes right". A good way to deliberately create an emotional disconnect is to hide a characters eyes entirely.

Windows to the Soul is when this happens with eye color.

Has no relation to Mac of the soul or Linux of the soul.

Examples of Windows of the Soul include:

Anime and Manga

A visual, literal example in Ushio and Tora - the eyes 'shatter' to become pupil-less when a user of the Beast Spear's soul is fully consumed, just before they transform into a full monster.

Comic Books

Played with in the 'Shining Armor' story from Astro City. Irene sees a glint in Atomicus's eyes, which she initially reads as a challenge, leading her to prod him about his secret identity until he leaves the planet, after which she understands it was fear. It seems more probable that the glint is just a glint in his eyes she can read however she pleases. He is radioactive.

Literature

Harry Potter is the former Trope Namer, for the infamous "glint of triumph" Harry sees in Dumbledore's eyes in Book 4, which tipped everyone off that it's a huge setup.
Percy Jackson and The Olympians is only too guilty of this.
Juliet Marillier's books do this all the time, sometimes with more than one emotion at once, thus: "She saw a mixture of triumph and dread in his eyes."
The last line of Richard Matheson's "The Splendid Source": the hero has just been invited to join the Ancient Tradition he's been tracking down throughout the story. He's all but speechless ... "But, already, the light of consecration was stealing into his eyes."
Danny, the Champion of the World is one of many works to discuss the phenomenon of the "eye smile" - twisting the corners of your lips upwards looks nothing like a real smile unless the eyes are doing the right thing (which in real life is probably squinting slightly rather than reflecting the innermost workings of the soul, but Truth in Television nonetheless).
A major theme of Coraline, where the Other Mother has button eyes and wants to give Coraline the same.
In The Dresden Files, wizards can see a person's soul with their Sight if eye contact is maintained (this is why you don't look at a wizard too long. They see too much). However, there are three drawbacks: the other person can see yours too, it only works once, and you can't forget what you see. Ever.
In The Lord of the Rings and the supplementary material, attention is often brought to Elves' bright eyes. From the descriptions they seem to invoke borderline Uncanny Valley in some characters, and especially evil-leaning characters are terrified from looking Elves' in the eyes, and even good-aligned mortals feel awe from them. The supplementary material explains explicitly that the fire of the Elvish spirit shines through their eyes much more strongly than mortal spirit.
In the Wheel of Time series, characters get a hint that someone is evil or deceptive because they have a smile that does not touch their eyes. In truth, a genuine smile does contort the eyes, and it is apparently impossible to fake this.

Live Action TV

Babylon 5: In the first episode when Ivanova is telling Talia about what happened to her mother, she says "the light in her eyes went out, bit by bit".

Music

Eyes by Kaskade featuring Mindy Glendhill features the trope's name right in the chorus.

Video Games

"I swore I saw a glint of satisfaction in Kain's eye when the Soul Reaver was destroyed."