Survival of the Fittest has a couple of these moments. On the V3 island Bobby Jacks puts his desginated weapon (a syringe) to use by sticking it straight through the eye of Tyson Neills. Shameeca Mitchell also killed Boxer Carvalaho like this, with a customised toothbrush/dildo, by stabbing him through the eye and then smashing his head in with a wrench. (No, seriously)
JR Rizzolo's torture of Laeil Burbank, during which he cuts out her left eye with a sword and crushes it with his bare hand.
In SotF Evolution, Billy-Jay Clarke's power is of 'Ocular Luminescence' (torch beam eyes, effectively). However, the feedback loop of said power is flawed and he absorbs so much solar energy that it overloads and his eyes melt.
A particularly squick Eye Scream occurred recently in V4 when Maxwell Lombardi jams both his thumbs into Daniel Blessing's eye sockets... Ouch.
Rekka Saionji is on the receiving end twice in the same post, in the same eye, first from his opponent's elbow, then from his tooth.
Gaia Online recently introduced the ability for Avatars to purchase new eyes... from the Hair Salon.
Vanessa: Doing eyes isn't too different than doing hair, I guess. Just a lot of snipping and drying and jars of blue stuff.
Older than that is the Oculus Mythica, an item that gives you a bunch of unique eye designs to choose from. Including empty, bleeding eye sockets. Funny, people don't approach me often when I wear that item.
In Mur Lafferty's podcast fiction series Heaven, a character named Daniel loses the same eye repeatedly during the course of the series.
Jordan Eats Normally Now, of The Fear Mythos, has an all-but-shown case with Nathan in this video. You can see Sam grab a pencil, you can hear disgusting squishes in the struggle, and you can hear Nathan shout "MY EYE!" note Later entries confirmed he was stabbed in the eye. He showed up later with an eyepatch, too, which was awesome.
Fivesecondfilms made a series of films (all 5 seconds long) dedicated to eyes and, more often than not, the mutilation and/or removal of them. Check it out here. Don't worry, it's nowhere near as horrific as it sounds.
The character of Galaxy from Equestria Chronicles accidentally teleported her eyeballs out as a foal.
This picture pulls it off in a creepier way than most ever want to see.
Tokyo Magic Star: In episode 4, Sakura attacks a villain with magic. Seems standard for a Magical Girl... until it makes his eyes bleed.
On the Ask Hobo Pony blog, the eponymous character has a glass shard stuck in her eye that she doesn't notice until commentors point it out. She's given a choice of a lollipop, a pencil, and a pair of tweezers to remove it; rather than make the obvious choice of the tweezers, she tries to use the pencil to dig it out which exacerbates the problem when it also gets stuck, so she has to go to a free clinic to get both the pencil and the shard forcibly pulled out.