A manga scene where Kiriyama casually pokes out the eye of the class' former PE teacher, grabs the hanging eyeball and squeezes it definitely takes the cake. The whole scene is exhibited with rather elaborate, graphic panels and Kiriyama's disturbingly calm remarks.
"It's like egg whites"
There is a particularly disturbing eye scream in Battle Royale II where one girl's eyes are shot out by a sniper and she flails about wildly screaming for her best friend, who is in a nearby naval boat screaming for her - then the blind girl's boat explodes.
There is a particularly disturbing scene in the manga involving Mitsuko and Yuichiro. Yuichiro is dying of a bullet wound, and Mitsuko, who is somewhat deranged at this point after killing Tadakatsu and has regressed to her fucked-up childhood, decides to make him better...by raping him. Yuichiro begs for her to stop, as she is hurting him, and Mitsuko responds by stabbing the poor little guy in the neck with her sickle, seeing his cries of pain as a betrayal. As he dies, she is shown as a giant, damaged version of the doll her father gave her, asking, "How do you like my eyes now?"