The Darkest of the Hillside Thickets song "Tarred and Feathered" is about a torturer talking about his favorite activities (or perhaps receiving advice from monsters, it's kinda vague) and includes the lines "Here's some silver fishhook/To slip in their eyes" and "Here's some metal cubes and jacks/Force them in their sockets".
"Debaser" by The Pixies was inspired by Un Chien Andalou, thus explaining the lyrics "Slicing up eyeballs/I want you to know" and at a later point, "Slicing up eyeballs" followed by Francis' insane laughter.
Garbage's video for "Blood for Poppies" has the lead singer Shirley Manson having her left eye slit open in homage to the aforementioned film.
Megadeth's song "Sleepwalker" is about a person who murders people in his sleep/dreams and contains the line "here's some toothpicks for your eyes!"
Alice in Chains' video for their song "Man In The Box" has a guy walking around with his eyelids sewn shut.
According to the backstory of Gorillaz, 2D suffered two car accidents in a year. Each left him with an eight-ball fracture in one eye. Now he's stuck with a pair of creepy Black Eyes and the nickname "2D", short for "Two Dents".
The video for Skinny Puppy's "Worlock". Full stop.
Averted in "Re: Your Brains" by Jonathan Coulton. All they want to do is eat your brains. They're not unreasonable. I mean, no one's going to eat your eyes.
Arrow to My Drunken Eye by Carla Bozulich / The Geraldine Fibbers. "I'm censor [sic]. I'm optic. I'm a lake at high noon, glittering ripple rip open cocoon..."
Creature Feature's song ''A Gorey Demise'' lists causes of deaths of twenty-six persons, listed in alphabetical order, giving a chilling example of this trope: E is for Erik who was buried alive/ F is for Frank who was stabbed through the eye
Florence + the Machine's song Girl With One Eye. "I took a knife and cut out her eye/I took it home and watched it wither and die/she's lucky that I didn't slip her a smile/but now she sleeps with one eye open/'cause that's the price she paid."
Angel of Death by Slayer is actually about Dr. Mengele, but it incorporates some lovely lyrics about abacination (pressing hot metal to someone's eyes).
No More Me by King Diamond from the concept album "The Puppet Master", features the titular villain removing King's eyes and placing them into a puppet.
Harvester of Eyes by Blue Öyster Cult is about a monster that goes around killing people and taking their eyeballs.
Queen's Bohemian Rhapsody has the line, "So you think you can stone me and spit in my eye?/So you think you love me and leave me to die?" This may have been meant figuratively, but hey, it's Queen.
Savlonic's music video for their song Wandering Eye qualifies, BIG TIME. While the song is about a boy who catches his girl friend looking at other people, the creators of the music video made her eye literally pop out of her head and start wandering around. It even starts dragging her across the floor!
God Module, Victims Among Friends: "You don't need your eyes any more / open them to see me rip them out."
Ayumi Hamasaki's music video for Brillante. The claws worn by the 'consort' are hinted at to be the cause of her Tears of Blood.
At the beginning of the Austrian Death Machine album "Double Brutal", in the dialogue between "Ahnold" and "fake Ahnold" (it makes sense in context, kind of): "I will burn your eyes out with my stogie, you idiot!"
