Windows to the Soul

Now what could her element be, I wonder?

In her eyes I see the sky and all I'll ever need
In her eyes time passes by and she is with me

—Josh Groban, "In Her Eyes"

This is where a character has eyes that are a color representative of that character, such as if a character who is heavily associated with water has deep blue eyes, or someone associated with fire has red or gold eyes, ect. Sometimes, a character's eye color is practically their one defining trait, such as if they are a spy or mercenary and wear a mask or something similar to conceal their faces, only able to be identified by another character by their eyes. Examples often include but are not limited to:

Red Eyes, Take Warning: often symbolizing a character who is evil. If they are not evil, they may be closely related to fire in some way, either wielding that element as a weapon or simply having some kind of association with it.
Blue Eyes: Depends on the shade.
- Light or Icy Blue: Can be representative of Air or occasionally water, if wielded as Ice. Sometimes given to a villain to show how cold they are inside. If redeemed, the villain's eyes will often be portrayed as a darker, deeper blue. Sometimes given to a good character who is not elementally based as a sign of purity or innocence.
- Deep Blue: Usually shows the character's association with water. Can often be given to healers or clerics, as healing is typically associated with water. Also given to some non-elementally powered characters as a way of showing how deep their souls are, or that they are a character who gives emotional healing and such. Rarely given to villains.
Brown Eyes: Usually associated with Earth. May represent a character who is down-to-earth, or full of earthly wisdom. Often a character who is good with animals, particularly if they are shy around other people, has brown eyes to make them look softer and more timid, like a deer. Can make for some killer puppy-dog eyes. Often given to children or young adults who are still very childike in some ways to show innocence.
Green Eyes: Also usually associated with Earth, but more plant-related than soil or stone. Characters with this may be wilder, display more uncontrollable tendencies and enjoy being outdoors, often barefoot so nothing comes between their bare skin and the plants they love so much. Sometimes used to show a character who is exotic and/or particularly sexy. Seductresses often have green eyes.
- Often given to villains to show how evil or different they are, as green is known as the color of envy and most villains are seen to be jealous, selfish individuals.
Silver Eyes: Sometimes representative of Air, but often used to portray purity of spirit. Healers, clerics, mages, wizards and other magic types, or elves, may often be shown as having these to show how different they are from 'normal' people, as silver or true gray eyes tend to be rare. Can often show a spiritual guide or prophet, or someone in a mentoring role. Gray eyes can also characterize a cold, strong-willed and unapproachable character often with an "ideas above people" mentality.
Gold Eyes: Often held closely to fire. May show a character who is uncontrollable, untethered or otherwise unstoppable in reaching their goals. Similar to Silver Eyes in that they are often given to 'special' people or races to show the audience that they are very different from everyone around them.
Hazel Eyes: Tend to fall under the same category as Green, though characters given these may be even wilder, or sometimes seeking to find who they are, as the mix of colors in their eyes can sometimes represent their mixed feelings or thoughts, displaying that they aren't entirely sure of who they really are yet. Upon discovery of their inner self, their eyes may stick to one particular shade.
Violet/Purple Eyes: Often a telltale sign of a Mary Sue in fanfiction, Violet or Purple eyes are incredibly rare, moreso than nearly any other color, and therefore are used to make the character seem more unique and show how special he or she is, how different they are. Females with this may be portrayed as gentle, wildflower-gathering maidens, even in a modern setting.
Mismatched Eyes: Similar to Hazel in that a character with these may not seem to know who they are at the beginning. Another trait usually associated with Mary Sue characters in fanfiction. May represent a character who happens to wield or be associated with multiple elements or powers, or who has a split personality, one eye being focused on more with one personality, and vice versa. One eye may be hidden under Blinding Bangs or something similar, the one which is visible showing which one happens to be in control at the time.

Examples of Windows to the Soul include:

Anime and Manga

Train from Black Cat has yellow/gold eyes. In the anime, both Saya and Creed tell him repeatedly that his eyes are so beautiful. And they both fell for him.
Honey-senpai from Ouran High School Host Club has light brown eyes, which not only helps him look even more innocent and childlike, but gives him heartbreakingly adorable puppy-dog eyes when he chooses to wield them. However, don't make him mad, because those typically adorable eyes can also be TERRIFYING.
- Kyouya has gray eyes and considering he's the "Cool" type, it's fitting.
- And Tamaki, the Host King, has purple eyes. It's also very fitting for his personality.
The gray-eyed, pupil-less Hyuuga family from Naruto fit the seer — they can see a lot more than normal, including through matter or behind their backs. They have the unapproachable, "ideas above people" mentality of the second gray eye type. Neji Hyuuga, who was a hardened fatalist before his Warrior Therapist session with Naruto certainly fits. Hinata Hyuuga though, has the eyes but her personality is the absolute opposite.
All Claymores have silvery-gray eyes. In fact, their eye color is what most commonly gives them away when they go undercover. Needless to say they are mostly very stoic (except for Psychopathic Woman Children).
Both L and Near of Death Note have gray eyes, though L is arguably a more apt example of this trope.
- However, it should be noted that L's eyes are only gray in the anime; they are black in the manga.
Fakir from Princess Tutu has green eyes to match his hair. He definitely fits the "exotic and sexy" implication of the trope...and he inherited Drosselmeyer's Rewriting Reality powers, so he fits the magical implications as well.
Rina of Mermaid Melody Pichi Pichi Pitch has these eyes while in mermaid form or her Magical Girl form. In normal human form, she has Gray Eyes.
- By extension, all Green mermaids like her have these eyes, but they are just a racial trait, as mermaids are Color Coded for Your Convenience.
Edward, Alphonse (when he's human), and Hohenheim of Fullmetal Alchemist all have gold eyes. This is an ethnic trait of the Xerxesian race, of which Hohenheim is the last full-blooded member; his sons, though only half-Xerxesian, inherited their coloring from him.

Comic Books

Storm of the X-Men is often portrayed with either eyes that are always Silver/Icy Blue, or become either Silver or White when she summons her ability to control the weather.
Doctor Strange from Marvel Comics officially has gray eyes. They're often depicted as blue or even green, however.
Among the many green eyed redheads from the Marvel universe, Mary Jane Watson from Spider-Man is given these to make her not only more attractive, but giving her a safely exotic yet still familiar girl-next-door flair.
Catwoman has always had green eyes canonically, though she has been played by non-green-eyed actresses; she fits the concept to a "T", being mysterious as she is, and associated with cats, who sometimes have vivid green eyes.
Poison Ivy usually boasts the typical green-eyed redhead combo, showing not only her exotic, mysterious beauty, but also her association with plants.
- They aren't the only Batman characters with green eyes, either. With respect to different artists, The Joker is often portrayed with green eyes (the shade varies) when a close-up of them is shown. This is of course going more with the "untrustworthy" and "spitfire" aspects of his personality, since he doesn't technically have any superpowers besides insanity (or sometimes, "super-sanity"). It could also be to match his hair color or to tie him into his chemical bath-based origin...
Leetah from Elf Quest has green eyes. Also quite a few other elves, including the plant-shapers Redlance, Goodtree and Kaslen, fitting the "natural magic" bit.
Oliver Queen, a.k.a. Green Arrow, a modern-day Robin Hood, has green eyes, which he has passed on, somewhat improbably, to both of his sons. Including the adopted one.
In the comics, it's revealed that Demona from Gargoyles has green eyes, reflecting her mysterious and exotic nature. (It was hard to tell in the animated series).
The Hulk is often shown with green eyes, especially in recent years, though in the past they've been red. Bruce Banner, on the other hand, is more often shown with brown or blue eyes, the change to green being the signal that running might be a good idea.

Film

In Disney's Beauty and the Beast, when the Beast is restored to his original form as Prince Adam, Belle does not recognize him until she looks into his deep blue eyes, the exact same shade they were while he was the Beast, and then recognizes him immediately.
Doctor Calico, the villain of the Show Within a Show from Bolt has green, catlike eyes, and is often referred to as "The Green-Eyed Man".
Scar from The Lion King, who was jealous of his brother's power, particularly after Simba was born, which ensured that he would never take the throne by reasonable means, had vivid green eyes to show his jealousy.
Esméralda from the Disney adaptation of The Hunchback of Notre Dame possesses the positive, exotic qualities, and her name even means emerald.
- She, despite being the film's heroine was actually also modeled after several female villains from earlier Disney films, who all have green eyes, so that she will actually be portrayed as being evil by Frollo, the film's real Big Bad, while to the viewers, she's actually on the side of good. This is actually done to show the fact that she is hated by the villain because he thinks that she is evil even though she really isn't.
- In the -shudder- sequel, her eyes were changed to a soft, gentle blue, her skin tone lightened drastically and she started wearing shoes, despite never having done that before as part of her wild nature, most likely to show her as a softer mother figure rather than the untamed gypsy wildcat she'd been before, since she and Phoebis had a son now, and she was no longer the female lead, thus needing to be able to fade into the background.
According to The Jungle Book 2, Shanti (the girl who led Mowgli back to the Man-village with her singing) has "big, brown eyes." This is possibly to show that she is the one who returns Mowgli to his roots, grounding him in the fact that he is human, and nothing can change that. Granted, none of the human characters in either movie appeared to have any color other than brown, so it was possibly just because of their race.
Mother Gothel from Tangled was cold, manipulative and filled with steely determination to keep her youth and eternal life no matter what, and was given gray eyes to show this. Rapunzel, an earthy young woman who becomes a bit wild (at least for the time, and compared to what she was before) with her first taste of freedom, has green eyes, and also runs around barefoot.
Megamind, an alien from another world who is decidedly different, has bright green eyes to show how unique and unusual he is, though it's hardly necessary. It also becomes a way of telling it's him when he's sometimes disguised.
Aisling from The Secret of Kells has green eyes, which fits the "magical" aspect of this trope since she's one of The Fair Folk. She's also something of a Nature Spirit, being fiercely protective of the forest outside Kells.
The Mad Hatter, in Tim Burton's Alice in Wonderland, has extremely bright green eyes, though they turn a disturbing reddish-gold when he's agitated. The Cheshire Cat also has unnervingly huge green eyes, both showing how wild the characters are.
Loki, in Thor. Most noticeable in the posters, not only showing his status as one of The Fair Folk, but how wild and uncontrollable he is.

Literature

Harry Potter The fact that Harry Potter and his mother, Lily, who had red hair, both have vivid green eyes is emphasized repeatedly. With good reason.
- Albus Severus Potter, Harry's middle son, is described as the only one of his children to have inherited their grandmother's eyes, completing a rare triple- Generation Xerox.
- Hermione Granger has brown eyes, showing that she is one of, if not THE most down-to-earth character in the series, grounding the rest of her group and often being the mediator between Ron and Harry's scuffles.
- Ginny, Ron's little sister and Harry's Love Interest, also has brown eyes, perhaps representing how she emotionally grounds Harry, as she is the only romantic interest he's had who has been as solid, lasting presence in his life, the rest of his love interests being flighty, sobby, or otherwise unbalanced emotional wrecks that leave Harry worse off than he was to begin with.
- Luna Lovegood has protruding silver eyes, probably meant to be reminiscent of a full moon (hence lunacy), although Fanon often makes them silvery blue.
- Draco and Luscious Malfoy both have gray eyes of the cold, steely variety.
Discworld's Tiffany Aching and Agnes Nitt are both sensible and brown-eyed.
- Something of a subversion in that sensible, down-to-earth people often make for talented witches such as Agnes and Tiffany.
  - In one of the early books, Pratchett states that Lancrastrians, emigres often becoming very successful witches and wizards among other things, are very down to earth, saying that only those who are firmly grounded can build castles in the sky. One could say this reflects magical power, until you realize that Granny Weatherwax has blue eyes. Though this could have something to do with the fact that she tends to ignore expectations.
Since stoicism is the norm for heroes in the Middle-Earth, gray eyes (said to be a racial trait of, among others, the Noldor elves and the Númenoreans) take up a very large chunk of the Lord of the Rings good guy population. The fact that Tolkien's beloved wife Edith was gray eyed is probably also pertinent.
The protagonist of the children's novel The Girl With The Silver Eyes is telekinetic, and she and other children who received strange powers because of a medical experiment performed on their mothers all have this eye color.
Sherlock Holmes possesses Gray ( or 'steely') eyes of the piercing variety. His brother Mycroft's are of a "peculiarly light, watery gray".
In A Song of Ice and Fire, cold, gray eyes are a genetic trait of the Stark family line, reflecting their stoic nature and hard life up in the North. Ned's and Jon's are frequently focused on. Arya seems to be the only one of Ned's trueborn children to have inherited the eyes, as the rest take after their mother.
Gregori from the Dark series is a healer with an unapproachable personality and the ideas-above-people mentality. A great deal is made about his silvery eyes.
- Incidentally, Xavier, the main villain of the series, shares the eye color. It is implied that silver eyes are a consequence of experimenting with darker or forbidden forms of magic.
The elves in the Bordertown Shared Universe all have silver eyes, and nearly all of them are relatively cold and intellectual.
The Herons (Geoffrey, Christopher, and Cecily) have gray eyes and "tawny-yellow" hair in Elizabeth Marie Pope's The Perilous Gard. Geoffrey's are described as "level and rather forbidding", and he is described several times as resembling granite and steel in character. Christopher eventually reveals himself to possess a warmer, rather impulsive, nature, but he too is cold and remote when the protagonist Kate first meets him.
The Haldane kings in the Deryni novels all have gray eyes.
- Not just the kings. Prince Nigel (Heir Presumptive and frequent Regent), his sons, even cousin (and Queen by marriage) Araxie. In Conall's case, the cold and strong-willed aspects of his character could be signaled by this.
  - Also, Alaric Morgan has gray eyes and blond hair. He does serve as a mentor for Kelson, and he's actually innocent of the evil motives (and most of the deeds) ascribed to him. Danger and ruthlessness also factor into it, however, since he actively cultivates a dangerous reputation, and he has plenty of martial and magical skills to back it up. To top it all off, he's a devoted servant of the House of Haldane, so having the same colour eyes serves to point up that association.
Senna Wales of the Everworld series. Solidly type 2 eyes, "the color of rainclouds" and a personality to match. Her mother, who briefly appears in the ninth book, also has gray eyes, but doesn't really fit any of the personalities associated with it.
Cordelia Naismith Vorkosigan has gray eyes, of the storm/sea variety, foreshadowing her soon to be infamous temper. In her later years, she becomes renowned for her strength and calm, not to mention her marriage to a man named for a sea (Aral Vorkosigan)

"Look at her eyes. A man could drown in those sea-gray eyes." (Aral, in Barrayar)

Polgara of The Belgariad books tends to have gray eyes (that can change to blue with her mood). She certainly fits the first example of someone wise beyond their years (though she's 3000 years old), and when they're "steel gray", it usually means she's determined enough to fit the second type...not to mention royally pissed off.
In Peter S. Beagle's novel The Last Unicorn, Schmendrick the Magician is often mentioned as having green eyes, covering the magical aspect of his character.
Percy from Percy Jackson and The Olympians has sea-green eyes, because he is the son of the sea god Poseidon.
In Devon Monk's Dead Iron, Wil's eyes are still copper even in wolf form. The precise color is not so significant as what it shows about Wil's ability to keep his human mind in wolf form.

Live-Action TV

In a subversion, River Tam of Firefly has brown eyes, which typically display stability, when she is anything BUT stable, mentally or emotionally.
Djaq from the BBC's Robin Hood had large brown eyes, was a wise and stabilizing force in the outlaw camp, and had a wounded puppy-dog look that could tear your heart out. Notable mainly because almost everyone else in the cast had Blue Eyes.
Glitch of Syfy's Tin Man has big brown eyes. They're a sign of his trustworthiness and bravery, since he's anything but stable.
Neil and Mike of The Young Ones both have brown eyes. Out of the four flatmates, their personalities are the most low-key and down-to-earth — well, as down-to-earth as you can get on the show — and contrast wildly with those of the noticeably younger, Hot-Blooded Rick and Vyvyan (who both have blue eyes).
Hurley of Lost has brown eyes and is one of the most stable of the Losties. Jack, the physician and leader, also has brown eyes.
Niles Crane on Frasier in contrast to his brother's Blue Eyes — while he is more rigid, neurotic, and fussy than Frasier, he is more down-to-earth and practical, (not to mention Woobieish), and often plays Straight Man to his brother's overblown, self-deluding shenanigans.

Mythology

Athena, the Greek goddess of wisdom, has gray eyes. A frequent epithet in Homer's The Odyssey even refers to her as the "gray-eyed goddess".

Video Games

In a setting that is filled to the brim with blue, green and yellow eyes, the only two original characters that have brown eyes in the Kingdom Hearts series are Hayner and Pence, who are, fittingly, a pair of Ordinary High School Students.
Cream the Rabbit from Sonic the Hedgehog has big brown eyes, most likely to show how innocent she is amongst her admittedly violent surroundings.
Commander Miranda Keyes in Halo 2 and 3 has gray eyes as well, and is portrayed as being extremely calm and controlled.
Silver from Pokémon Gold and Silver has gray eyes as of the remakes. It's both makes him have a Meaningful Name and alludes to his cold personality.
Most of the cast of the Professor Layton games have relatively small, dark eyes. Flora, however, has huge saucer-like deep brown eyes, which just serve to further remind the player that she's the resident personification of sweetness and innocence.

Webcomics

The Regional Fairies who become humans in Gunnerkrigg Court have gray eyes as a sign of their origin. They're strong-willed, but hardly cold or unapproachable (and certainly not stoic), varying in their personalities between smiling tricksters and borderline-psychotic Tsunderes.
In Drowtales members of the Val'Beldrobbaen clan often have gray eyes. They have a goth-like attitude.
- The "to the soul" part is also literally true of tainted characters, since it shows that they've merged their aura with a nether being, willingly or unwillingly.

Web Original

Apollo, Artemis, and Athena in Thalia's Musings all have silver eyes. Apollo is a prophecy god, his twin sister Artemis is a deadly huntress and a sworn virgin, and Athena, also a virgin, is the Goddess of Wisdom and Battle Strategy.

Western Animation

Avatar: The Last Airbender:
- Katara and most other Waterbenders or members of the Water Tribe have deep blue eyes.
- Most Earthbenders or members of the Earth Nation have either green or brown eyes.
- Firebenders or members of the Fire Nation usually have gold eyes.
- Though we didn't see many airbenders in the series (what with them all being dead) they appear to have typically had gray or light blue eyes, as Aang had gray eyes.
Lisa, in The Simpsons, has gray eyes. She is probably closest to mentor, though does tend to think herself smarter than everyone else. No one would ever know it from the pupil-less animation; we only know because Milhouse does say her eyes match his gray safety belt.
My Little Pony: Friendship Is Magic:
- Fluttershy has soft blue-green eyes, probably indicating her connection with nature and healing, as well as her innocence and gentleness.
- Twilight and the Great and Powerful Trixie have purple eyes, Twilight being the embodiment of the Element of Magic itself, Trixie's sole talents appearing to be magical in nature, the color thus showing their far more magical nature among all the other ponies.