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.
As a result of an organ transplant from a ghoul, Ken Kaneki (Tokyo Ghoul) was transformed into a human/ghoul hybrid.
Upon his initial demise, Colonel Volgin's (Metal Gear) body was taken into Soviet custody and modified extensively, turning him into the nigh-unstoppable Man on Fire.
Touhou Fuhai (Rosario + Vampire) is the inventor of the Human Modification Technique, which reconstructs a human's cells to enable them to use yōjutsu...
...of which Tsukune Aono is the first success.
Chimera (Marchen Awakens Romance) used the power of Ghost ÄRMs to replace parts of her body shredded apart during torture.
General's (Marchen Awakens Romance) Ghost ÄRM, Gentatsu allows him to modify his arm depending on the side Pause's Ghost ÄRM, Verfile lands on.
Dr. Genus (One-Punch Man) is such an accomplished scientist in bio-molecular enhancement…
…that he was able to restore his lost youth among a host of other feats.
A brilliant master biologist with immense knowledge in genetics, Vinsmoke Judge (One Piece) was able to manipulate his children's DNA traits and enhance their bodies with powerful genetic enhancements.
Obito Uchiha's (Naruto) right side was implanted with Hashirama's DNA cells, which allows him to survive without food or water, heal rapidly and use Wood Release.
Madara Uchiha (Naruto) cultivated Hashirama's DNA, transplanted them into his body to enhance his power and modified and restored young Obito's permanently damaged body to optimal condition.
Shin Uchiha (Naruto) possesses a unique genetic make-up that will completely accept any new genetic material, be it tissue, organs or entire limbs, without a chance of rejection, allowing him to fully integrate it into his being.
Locke (Archie's Sonic the Hedgehog) performing genetic experiments on himself.
Hiei (Yu Yu Hakusho) had his Jagan Eye implanted in his forehead by Shigure the Osteopath, a doctor of darkness.
Master Hades (Fairy Tail) transplanted his heart into a magic generator called the Devil's Heart...
...enhancing his physical and magical abilities tremendously.