John Freeman fired his bullet from teh gun really fast and the bullets went and shot the final boss in the eyes and the final boss couldnt see.
In Land Before Time: Twilight Valley, a dinosaur gets his eye ripped out by another dinosaur, then nearly decapitated; this is after he was kneed in the groin. The less brutal "finger in the eye" attack is also used (by a clawed pterosaur on another pterosaur).
The protaganist of the Ranma One Half fic Be careful what you wish for winds up taking a knife to the eye. He later on is caught performing a self-inspection to check its condition. This is played for laughs, really.
In the sequel, A careless wish former protaganist's successor fights something big, purple, and mean. The words 'Occular Fluid' are used, and cover one of the character's hands. NOT played for laughs this time.
An unintentional example: Characters in (usually bad) fanfic being described as having "[food, precious stone or something equally silly] orbs" for eyes. Think about it...
In Tiberium Wars, a Nod soldier is hit by shrapnel in her eyes from a grenade, ruining both her eyes and her face. This becomes a minor plot point later on when the Nod commander, Rawne, opts to give her advanced cybernetic eye replacements and transfers her to his personal command.
The fic "Alpha" for that fandom leverages this trope pretty well in one of the later chapters. (It's also well-handled Dark Fic, but in all likelihood not SFW. Mentions of Villainous Incest at the start of the second chapter might warn you.)
In Ash the Wanderer's Dragon Ball fanfiction "Atrocities," original character Erik tells the Son brothers of replacing his love interest's eyes with those of a mad scientist using a machine the scientist created after her own eyes were destroyed in an explosion. Not quite as squicky as it could be, but the gore in the rest of the fic more than makes up for that.
The Halo fanfic "Enemy of my Enemy". When the Pride of Sangheilos crashes on Crassus, one of the crew members comes up to his commanding officer with one eyeball gone, burst during the impact. He treats it as if he just got a haircut.
There are at least two Harry Potter fics that I know of that used this trope. But there are probably more.
Like Shadows on the Winter Sky by Resmiranda: In chapter 3 you find out that Snape is getting tortured after being found out to be a spy, but the reader is left unsure as to how. Then chapter 5 comes along, in which the reader is told exactly how his torture proceeded. Voldemort took the knife mentioned at the end of chapter 3 and plugged it into his eye sockets to remove his eyes. After that is done, Voldemort makes sure that Snape can never be fitted for a prothesis by placing his wand into the sockets and firing off a curse that completely damages the nerves that runs from the socket all the way to the occipital lobes in the brain. At the end of the chapter, Snape is back at Hogwarts, confined to his rooms. While there, he decides that it will be a good idea to plunge his own fingers into his bloody sockets and use said blood to write morbid poetry on the wall.
Another fic had that Snape was once again found to be a spy and tortured. When he returns to Hogwarts it is immediately apparent that one of his eyes can't not be salvaged. However, there is a slim hope that the other can. Well, that hope was for naught because when the bandage is removed from the remaining eye, the eye leaves the socket, slides down Snape's cheek and either falls into his lap or onto the fall. In other words, the bandage was the only thing keeping the eye in place. (If I recalled the name of the fic, I would put the name here, but I can't.)
In the Harry Potter fanfic Walk the Shadows by jharad17 after Harry pisses off Nott, a Death Eater, Nott responds by casting a spell which damages Harry eyes and removes his tongue.
The villain of Awakening, an Axis Powers Hetalia fan fiction, is real-life Nazi doctor Josef Mengele, whose many twisted interests included trying to change people's eye color with dye injections. The scene depicting such a surgery made even the author cringe while she was writing it.
The dark BL Death Note fanfic Poison Apple provides an example of this trope when Light gouges his own eye out with a piece of shattered mirror.
In the second part of Metal Gear Solid: Fight of Metal Gears, Jake Snake gets shot in the eye by Revolver Ocelot, and immediately puts on an Eyepatch of Power.
In the Left 4 Dead 2 fanfiction Two Step, Nick loses an eye when he saves Coach from a Witch. He is very obviously disadvantaged by it, being a survivor in a zombie apocalypse who's main defense is a gun. He's still a badass.
In the Mass Effect fanfic The Council Era, a batarian commander (whose species possesses two pairs of eyes, one above the other, for the record) serving under the Villain Protagonist is described as only having two working eyes. This was explained on his article page at the Mass Effect Fanon wikia. During his service for the Hegemony's military, Nikhail (the batarian) was taken prisoner by guerrilla soldiers, and when he steadfastly refused to give information for three months, they resolved to execute him before he could be freed by the Hegemony. He was in fact rescued, but not before his eyes had been stabbed out with a hot poker.
In the The Hunger Games/Hetalia crossover What If, one character, driven mad by guilt, will do anything to keep herself from seeing hallucinations of the one she killed. So she ends up (accidentally) wedging a rock in one eye and (purposefully) gouging out the other with the claw end of a hammer.
A Hetalia doujinshi featuring the sweden/Denmark pairing portrayed Denmark as quite the insane Yandere for Sweden, and one of his first crazy actions was using his axe to injure Sweden's eyes when he merely insinuated that he may take off and leave the Nordic group. Sweden managed to escape the worse part of his ire, but still had some damage to his eyes; in the next scene, he's seen using glasses.
In Poké Wars: The Exigence, Banette burns out a Golem's eyes (and everything else) with Will-O-Wisp. Also in the same story, Alpha Houndoom headbutts a Golem just so hard that its eyes rupture.
In Poké Wars: The Subsistence, Tracy stabs a Beedrill in the eye with a stick.
In the Homestuck RP New Game Plus The RPG, eye injuries seem to be a recurring theme. Near the beginning Kevin Low burnt out an imps eyeballs with a lit cigar to prove a point to his rival/enemy Jack and other imps. THEN he beat an ogre by jumping up to its head, and shooting his duel revolvers directly into its eyes. and THEN during a possession he has a monsters tendrils stab him through the eyes and take over his body.
In the fic Raccoon this occurs with both eyes. One of which is with a corkscrew, which get slid under the eye, and screws up the nerve endings attached to it before tearing it out. The other? Just ripped out
In the crossover fic Blood That Flows, Cinque uses her Rumble Detonator IS on Laevatein while Signum was holding it. The resulting explosion not only took her eye, but her hand and Laevatein as well.
Yet Again: Waltz tears out a rogue Hyuuga's eye, in front of a mirror.
Connecting The Dots is not very kind to its characters' eyes. Sasuke loses one of his eyes in a fight with Kyuubi-Naruto, Neji shoots a Kryptonite-tipped arrow into Bizarro's eye, killing him and Lex Luthor /Darkseid rips the Mangekyou Sharingan out of Kakashi's head to complete the Anti-Life Equation.
The Immortal Game: GeneralEsteem inflicts this on Twilight Sparkle by ramming an Artifact of Doom called the "Sliver of Darkness" into her eyeball, allowing a demon sealed within it to possess her. Much later, after regaining her body, she repays the favor by driving an even larger metal shard into Esteem's eye, through his brain, and out the back of his skull after he boasts about how he tortured, killed, and ate Spikenote though this turns out to be a final, spiteful lie.
Twilight also loses an eye in Mirrors, the sequel to Prince Charming, when Pinkie Pie's vengeful ghost carves it out with a knife.
Ryo (after a major crisis has just been averted): So…what's for dinner? Owww, Rika! Stop it, it hurts! Ouch, my eye!
In the Dark World of the Pony POV Series, Rarity ends up doing this to Fluttercruel during their duel — Fluttercruel manages to immobilize Rarity by using the Stare inherited from her "mother", and is about to finish her off when Rarity manages to telekinetically launch her fragment of Tom through one eye and then out the other. The Elements of Chaos can heal, but Fluttercruel is distracted long enough for Rarity to strike a more fatal blow.
In the Jackie Chan Adventures fic Queen Of All Oni, Jade has a moment of this, after being captured by the Smug Snake / Squishy Wizard Lung — he traps her astral form, contained in a body of shadows, in a glass sphere and gives her the "tanning session from Hell", using industrial-strength lights to torture her until she submits, at one point MELTING HER EYELIDS! After he's Killed Off for Real when she is rescued, she recovers somewhat, but her eyelids are now transparent, forcing her to wear a blindfold to give her some darkness when she blinks.
Hivefled; a risk of punching someone who's wearing glasses.
In A Growing Affection, Madara can take over someone's body by having his own disembodied eyes burn their way into the victim's eye sockets, and then connecting his optic nerves to the victim's.
In Harry Potter and the Something Something when a Parody Sue appears in Voldemort's lair offering him a shot at redemption Voldemort is entranced by her pretty eyes... the Sue ends up dead like all the others that keep showing up on Voldemort's doorstep but Voldemort kept her pretty eyes to play with.