Ashley "Ash" Williams (The Evil Dead); replaced hand with a chainsaw
The Grox (Spore)
Cyborgs (Civilization 4: Beyond the Sword)
Colonel Volgin/Man on Fire (Metal Gear Solid V: The Phantom Pain)
Ghost ÄRMs (Marchen Awakens Romance)
Sosuke Aizen (Bleach) has done immense research on Hollows, allowing him to give Shinigami Hollow powers such as a Hollow Mask and even a Resurrección.
The Vizards (Bleach) were among the numerous Shinigami who fell victim to Aizen's Hollowfication experiments, through extensive training they attained full control over their Hollow powers.
Kisuke Urahara's (Bleach) Bankai, Kannonbiraki Benihime Aratame, can instantly and flawlessly restructure and modify physical bodies, enhancing physical strength and restoring lost organs and appendages.
Pernida Parnkgjas (Bleach) can continuously evolve and modify itself with all the information gathered from each target its nerves touch.
As a result of experimental medical procedure, Peyton Westlake (Darkman) has no nerve endings, making him immune to pain, and causing adrenaline to flow through his body unchecked, increasing his physical attributes and leaving him emotionally unstable.
Professor Pyg's Dollotrons (DC Comics) were once-ordinary people who were modified by extensive surgery.
Frost (Dragon Ball Super) has modified himself to possess poisonous stingers in his wrists.
Doc Benton (Supernatural) regularly transplants others' organs and body parts onto himself.
In addition to replacing his left hand with a mechanical one and installing a clockwork heart, Karl Ruprecht Kroenen (Hellboy/BPRD), suffering from severe "surgical addiction," performed surgery on himself to remove his own eyelids, lips, and finger and toe nails.