Body Motifs

Most viewers will wince when they see a wound inflicted on a sympathetic character, since physical injury is something all people can relate to. For similar reasons, a motif that involves a part of the body is a particularly visceral one.

Usually, using a body motif means constantly referring to the body part in question (those who have to stop and retrieve their minds from the gutter may do so now). This can be done through dialogue or by physically highlighting it (such as someone who's constantly wringing their hands or tapping their foot). A tattoo, scar, piercing, birth mark or mole on a certain part of the body is another way of drawing attention to it.

Like most motifs, the symbolism is normally dependent on the associations most people have with that particular part. The eyes, ears, hands, tongue and nose are all connected to the five senses. A person's back can be related to "backstabbing" or "turning your back on someone." The neck is usually seen as a vulnerable point - partly due to years of vampire tales, but also because that's where many predators aim for when taking down their prey.

Of course, if the body part in question has been separated from the rest of the person it belongs to, it's a given that there's a Poetic Serial Killer around. Giving some thought to which part of the body he uses as a "trophy" is usually a clue to his motives.

Anime and Manga

 * CLAMP loves making characters lose an eye, to the extent that it has become something of a running joke in the fandom. So far, the count goes: in Tokyo Babylon,  in X1999,  in Tsubasa Reservoir Chronicle and  in Xxx Holic.
 * You forgot from Wish, even if that happened off screen.
 * In Monster, Johan likes to tell people to shoot him in the head . This is done as a parallel to the beast from Revelation, as well as being imitated in a puppeteer's play later on in the show.
 * Another body motif is embodied in Tenma's hands, which are steady during surgery but shake before his attempt to.
 * As well as Lunge/Runge's hand, which moves as if he's typing whenever he is learning new information or recalling something he has already learned.
 * Neon Genesis Evangelion focuses heavily on hands, eyes, (usually symbolic) vaginas, and disturbing combinations thereof.
 * In particular, a wounded/damaged right eye and broken left arm is a recurring combination, to the extent that when Rei first appears in the OP a window pane is covering said eye and arm.
 * Fullmetal Alchemist has a focus on hands and arms, especially outstretched towards the sky. Many State Alchemists have their circles imprinted on gloves or tattooed to their hands. Edward has his automail arm and Scar has his right arm. Almost all alchemists normally perform alchemy by placing their hands on transmutation circles.
 * In addition every alchemist who had performed human transmutation must give up a part of their body symbolic of their motivations.
 * He also lost
 * The bonus OVA for Darker Than Black decides to goof around with this trope by making Hei's collarbone, of all things, a plot point.
 * Tengen Toppa Gurren Lagann uses faces as a motif (more so than drills) - all their mecha are designed as giant heads with limbs, creating a significant shift in the status quo when the Gurren Lagann becomes the first truly humanoid mecha. After the first Time Skip, civilisation has been rebuilt, with faces as a recurring motif in architecture - and finally, the Anti-Spiral mecha deliberately subvert this motif, being designed without a face or anything that might indicate that they were of this world.
 * Basilisk has a clear obsession with eyes. Three characters have magical powers based in their eyes much like the mythical basilisk. Four characters are blind, at least temporarily, and in every case the blindness is central to the story.
 * Letter Bee has two; eyes and hands.
 * Eyes: One of Lag's eyes was replaced by a piece of amber when he was a baby; Ninche and both have cat-like eyes; Dr. Thunderstone and  are missing one eye each; the twin gate keepers are missing both eyes.
 * Hands: several characters have oversized claws instead of normal hands. These characters include Niche, Hunt,, and Zeal.
 * FLCL has those eyebrows...
 * And hands, too. Hands must be popular in Gainax works.
 * Hands, big time, in Dawn Tsumetai Te.
 * Eyes: One of Lag's eyes was replaced by a piece of amber when he was a baby; Ninche and both have cat-like eyes; Dr. Thunderstone and  are missing one eye each; the twin gate keepers are missing both eyes.
 * Hands: several characters have oversized claws instead of normal hands. These characters include Niche, Hunt,, and Zeal.
 * FLCL has those eyebrows...
 * And hands, too. Hands must be popular in Gainax works.
 * Hands, big time, in Dawn Tsumetai Te.

Comic Books

 * In The Sandman, eye injury as a common motif has been commented on by the creator. The Corinthian, Fiddler's Green and the Ravens, the first murder of Abel we see, even Despair's constant picking at her face all count.
 * There's also the fate of one of the students in the boy's school full of... former students, in Season of Mists, if I recall. He died choking on his own vomit, as he informs us, and we see his eyeball hanging out of its socket down his cheek. Fun stuff.
 * It's played for laughs, though-- his eye doesn't pop out until he's smacked on the back of a head by a grumpy former headmaster.
 * And the girl in Preludes and Nocturnes who stabbed herself in the eyeballs with some sort of skewery things while being mind-controlled.

Film - Animated

 * In Finding Nemo, when a fish character is injured, the injury will always be on or on the area of the fin - analagous to the hand, anatomically speaking, but in practice bearing a greater resemblance to a damaged leg: Nemo's fin is shriveled due to an accident before his birth, Gil's fin is deeply scratched from an escape attempt, and even Dory's fin gets stung badly from jellyfish tentacles.
 * In Coraline, there is a lot of focus on the eyes, as unnerving and creepy as they are.

Film - Live-Action

 * In the films of David Lynch, injury to the head is very common. Especially in the appropriately titled Eraserhead.
 * In Red Eye, the camera has an appropriate fixation with Rachel MacAdams' eyes, which are gradually turning all red and veiny as she stays up all night. The camera also likes Cillian Murphy's eyes, which remain icy-blue.
 * Many films featuring Cillian Murphy focus on his eyes, because, well...
 * There are entire papers written on the use of eyes in Blade Runner. Certain movements (or lack of thereof) of the pupil as responses to emotionally provoking stimuli are how one recognizes a replicant.
 * In Hancock, Red, the villain, has his hand cut off by the Badass hero. From that point, Red is always associated with hands (mostly just for laughs).
 * In the Star Wars saga, the severing of the hand or arm occurs frequently. This is such a well known motif that in Episode II: Attack of the Clones Anakin's disarming is teased during the factory sequence before actually occuring at the hands of Count Dooku. In Star Wars the severing of the arm or hand of an adversary is the most common way to defeat an opponent without killing them, making Count Dooku's actions particularly significant.
 * Subtle and not-so-subtle references to the groin abound in The Big Lebowski - Whereas the titular Lebowski has his hands and/or a blanket over his groin at all times, the Dude constantly stretches out his legs as often as he can. Miss Lebowski has a whole conversation about how men are uncomfortable with the word vagina and yet bring up variations on the word penis at the drop of a hat. Plus the whole, "We'll cut off your CHONSON!" part. Supposedly, this represents each characters desire for power versus the power they do wield.
 * Manos the Hands of Fate. Done so (ahem) ham-handedly that the MST3K crew shouts "SEEN IT!" when the hand design on The Master's robes is not-so-subtly revealed for the umpteenth time.
 * In Chinatown, Gittes' nose is cut. Because the crooks found he was too nosy.

Literature

 * In the British murder mystery, Messiah, the serial killer brutally murders his victims,  and takes out their tongues, replacing them with spoons..
 * Not having seen this series, this troper can only speculate how much fun he had with
 * Jacob Have I Loved: Sarah Louise develops a theory that a person's hands, not their eyes, are the window to the soul.
 * C.S. Lewis' Till We Have Faces mentions faces frequently. Aside from the title, Orual's ugly face is compared with Istra's beauty and with the many faces of the goddess Ungit. For many years, Orual wears a veil.
 * In A Series of Unfortunate Events, eyes are a common motif. Olaf, the villain of the series, has a tattoo of an eye on his ankle, and other references to eyes are sprinkled liberally throughout the series, from an eye-shaped building in The Miserable Mill to an eye-shaped icon on a submarine's radar screen in The Grim Grotto.
 * Timothy Zahn often uses a hand-as-title motif in his Star Wars Expanded Universe novels. In The Thrawn Trilogy, Mara Jade was revealed to have been the Emperor's Hand, a sort of agent. In the Hand of Thrawn duology, characters speculate that the Hand of Thrawn is an agent like Mara or a superweapon; it turns out to be a five-towered fortress with a massive repository of Thrawn's greatest weapon, knowledge.  The Empire Thrawn set up out in the Unknown Regions is called the "Empire of the Hand". Most recently, in Allegiance, the five do-gooder renegade stormtroopers accidentally name themselves the Hand of Judgement. The 501st Legion, Darth Vader's personal Badass Army, is sometimes called "Vader's Fist", though to be fair the 501st is an Ascended Meme / Reverse Defictionalization and not Zahn's creation. At the end of Allegiance, the Emperor's Hand saves the Hand of Judgement from Vader by claiming them as hers, saying "You have the entire Five-oh-first. You certainly won't begrudge me my Hand of Judgment." Then she hears the five out, concludes that while they are technically deserters they are also good Imperials, and lets them leave, telling them to lose the name. There's only one Hand in the Empire, and she's it.
 * The Lord of the Rings does a rather subtle theme involving the senses. Most good guys, if they have heightened senses, have heightened sight and/or hearing. The bad guys on the other hand, (particularly the Orcs and Nazgul) have heightened smell, and are often either impaired in the light or even partially blind. The effect of this is giving a much more animalistic or uncanny feel to the bad guys, while the good guys have cleaner, more human senses emphasized. The major obvious exception is Sauron, whose symbol is the eye.
 * TS Eliot had a thing for talking about separate body parts, especially eyes, to symbolize what he viewed as the fragmentary nature of modern life. See "The Hollow Men" and "The Wasteland" for some of the more prominent examples.
 * John Singer's hands in The Heart Is a Lonely Hunter.
 * A Song of Ice and Fire: hands appear with near-monotonous regularity, often as the objects of injury and symbols of a character's power.
 * George Macdonald, in The Princess and Curdie, gave Curdie the ability to ability to tell what a living being was truly like by taking its hand, or other limb, in his own. The "hideous animal" Lina's paw feels to Curdie like "a child's hand"; his own mother's "horny, cracked, rheumatic old hand, with its big joints, and its short nails all worn down to the quick with hard work", feels like that of Irene's great-grandmother (implied to be an angel); the king's courtiers have hands that feel like the limbs of pigs or donkeys.

Live Action TV

 * In the show House, the titular character's leg injury serves this purpose.
 * Lampshaded by Caleb in Buffy the Vampire Slayer when he tells, "I hear you're the guy who sees everything," just before gouging out one of his eyes.
 * Lost devotes a lot of attention to eyes, such as episodes beginning with an eye opening, Locke's comment of having "looked into the eye of this island," and a tendency for Dies Wide Open moments. There's also a motif of lost limbs: Montand's arm, Martha Toomey's leg, Pierre Chang's arm, Ray's arm, etc. Then there's Mikhail's eye, which fits both motifs.
 * Not to mention the consistent attacks on John Locke's legs, which seems to connect to his self-perceived helplessness.

Music

 * This is also true in songs written by John Flansburgh, both in They Might Be Giants ("Contrecoup") and his side-band, Mono Puff ("Unsupervised, I Hit My Head").
 * The Paper Chase, by Word of God are "fascinated with the idea of hands as independent from their owners", with songs like "Goddamn These Hands (I Let Them Touch You)" "Where Have those Hands Been" "Wait Until I Get My Hands on You", as well as heads, eyes, hearts, arms, kidneys... In fact, their lyrics ARE this trope.

Theater

 * Samuel Beckett's classic absurdist play Waiting for Godot substitutes clothing for this purpose, but the association is still there: the high-minded Vladimir is always looking at his hat, and the humbler Estragon complains that his boots are too tight. Lucky also cannot speak unless he has a hat on.
 * Beckett invokes this trope often. Play consists of three heads sticking out of 3 foot urns and literally nothing else. In Not I, the only thing the audience ever see is a disembodied mouth that speaks rapidly for about 15 minutes.
 * In Hamlet, Hamlet's father was killed by having poison poured in his ear. This allows Shakespeare to sprinkle the play with such auditory references as: "So the whole ear of Denmark is by a forged process of my death rankly abus'd".
 * Sophocles' Oedipus Rex is full of references to eyes, sight and blindness; echoing Oedipus' fate.

Video Games

 * There are a lot of characters missing eyes in Metal Gear. The series is heavy on symbolism, so it's probably meant to mean something, but what that something is is left for fans to bicker over.

Web Comics

 * Gunnerkrigg Court places a lot of emphasis on the eyes: Reynardine possesses people through their eyes, it's been hinted that the fact that Annie wears eye shadow is significant, the local Green Lantern Rings are called "Blinker Stones," the forest is populated by "glass-eyed men," and several characters obscure their eyes--most notably Zimmy with her Hidden Eyes, but Mr. and Mrs. Donlan count too, with thick eyeglasses and Eyes Always Shut respectively. A supernatural Freak Out gives apparently permanent insomniac eyes. Could be connected with the themes of illusion, searching and "not seeing things clearly," which are big of the plot.
 * Regarding Annie's eye shadow: kohl (used, especially in ancient times, as eyeshadow), is also known as surma, and it is often prepared using the mineral antimonite.
 * Coyote can be identified merely by his eyes. They have a very, very distinctive pattern. His grin is also very distinctive and usually seen along with the eyes, but his eyes are enough to know it's him. He also takes great joy in using his eyes in weird ways... like juggling them.
 * Jeanne's green eyes match the green eyes of most of the robots,.
 * When was with Coyote, he repeatedly called them "wandering eye".
 * Likewise, Supernormal Step uses an eye motif. The Nameless, an anti-Henderson Security group, is represented by a stylized eye. This eye appears all over the place, including on background characters (for example, Akela, a minor character, is almost guaranteed to get more development because she wears The Nameless's eye). Cecilia, the most important character so far, wears more detailed eye imagery on occasion. One can theorize that this represents how the resistance has eyes everywhere.
 * In The Adventures of Dr. McNinja both Dan McNinja and Gordito possess the Mustache of Authority.
 * Order of the Stick:
 * Homestuck removes an arm and injures an eye of a harlequin doll within Act 1. Thereafter, the missing-arm-missing-eye pattern reoccurs again and again, usually with evil or morally ambiguous characters

Western Animation

 * Zuko in Avatar: The Last Airbender. Most or all of the character's self-worth and daddy issues are all tied up in his hugely noticeable facial scar.
 * This seems to be the entire idea behind the Crimson Chin Comic/Webshow Within A Show in the Fairly Oddparents. Aside from the eponymous hero and his Jay Leno-parody chin, nearly his entire rogues gallery is based on various body parts. This includes the Bronze Kneecap, Iron Lung, Copper Cranium, Titanium Toenail, Gilded Arches, Golden Gut, Brass Knuckles, and Hair-Razor.
 * This seems to be the entire idea behind the Crimson Chin Comic/Webshow Within A Show in the Fairly Oddparents. Aside from the eponymous hero and his Jay Leno-parody chin, nearly his entire rogues gallery is based on various body parts. This includes the Bronze Kneecap, Iron Lung, Copper Cranium, Titanium Toenail, Gilded Arches, Golden Gut, Brass Knuckles, and Hair-Razor.