Vargas (Marvel) claimed to be Homo Sapiens Superior.
The Crimson Commando (Marvel) is a mutant whose mutation keeps him in peak physical condition.
SOLDIERs (Final Fantasy 7) are infused with the cells of an extraterrestrial, enhancing their physical condition and overall physiology.
Isaiah Bradley (Marvel) was one of the first test subjects of an early Super Soldier Serum.
Solid Snake (Metal Gear) is well known as "the man who makes the impossible possible" due to his physical prowess and military career.
Miranda Lawson (Mass Effect) is genetically engineered to be the peak of human perfection.
The Point Man (F.E.A.R) is a genetically-engineered super soldier who possesses extraordinary reflexes and combat abilities.
Mega Man Volnutt (Mega Man Legends)
Tinisha Dolaira (The Young Guardians) has a superhuman physical condition that makes her superior to humans in every way.
Agent Bishop (Teenage Mutant Ninja Turtles)
Cole MacGrath (Infamous series)
V from (V for Vendetta). V has been augmented through an experiment that gave him his enhanced condition.
After going through Super-Soldier treatments, Deathstroke/Slade Wilson (DC) was enhanced beyond typical humans.