Gordon (Agents of S.H.I.E.L.D.) lost his eyes as a result of undergoing Terrigenesis to activate his powers.
Vanessa Brewer (Angel) blinded herself as part of her training with the Order of the Nanjin, which granted her the power to sense energy sources and motion in a manner far more accurate than ordinary sight.
Despite being blind, Toph Beifong (Avatar: The Last Airbender) is capable of "seeing" by sensing vibrations.
After losing his left forearm during the Eclipse, Guts (Berserk) replaced it with a metallic device known as the Cannon Arm.
Wonderweiss Margela (Bleach) has sacrificed all his intelligence and mental capacity in exchange for being able to seal the immense fire based powers of Ryūjin Jakka.
Due to his injured leg, Shuu Sakurada (Castle Town Dandelion) compensates via his ability to teleport, allowing him to continue living a normal life.
After losing his sense of touch, Peyton Westlake's (Darkman) body overproduces adrenaline, granting him superhuman strength and immunity to pain.
Having been deliberately raised to interpret body language as a first language, Cassandra Cain (DC Comics) is illiterate and barely able to speak, but as a trade-off, she can intuitively read body language and predict her opponents' attacks.
Majora (Dragon Ball Super) compensates for his blindness through a highly sensitive sense of smell.