I was just wondering if Marvel Comics has had any superheroes or villains whose origins begin around the period of the American Civil War. Also, as a corollary I'd like to know if any of them survive today.
Given the nature of immortality in the Marvel Universe, there were plenty of beings with superhuman vitality and immortality which might have been active during the Civil War period. When reviewed, most of the stories in the Marvel Universe has those groups lying low during periods of extreme human violence, such as the Civil War. See: ClanDestine
Of Marvel's most famous long-lived mutants, Wolverine most likely would have missed the Civil War by a decade; he was believed to have been born around 1887. Nathaniel Essex (Mister Sinister) was born in 1859 and Apocalypse were two long-lived human mutants who were active and stories exist of their exploits during the period of the Civil War.
Wolverine's (James "Logan" Howlett) date of birth is not precisely known but estimated to have been between 1886 and 1897, just missing the Civil War period.
Nathaniel Essex was a biologist born in 1859 and transformed into a metahuman being by Apocalypse.
Apocalypse (En Saben Nur) was born over 5,000 years ago in the Jordanian city of Aqaba.
One of Apocalypse's self-proclaimed "Final Horsemen" Famine (Jeb Lee) was from the Civil War era, and made his first appearance in the Marvel Universe in Uncanny X-Force Vol 1 #3 (2010). He was stolen by Apocalypse from the time-stream and locked away as a failsafe weapon. During the Civil War he was a spy and assassin who penetrated enemy lines pretending to be a drummer. His mutant power manifested when his family was killed and he could kill anyone who heard him play his drum. (Discovered by @Wang, added only for completeness; Good find!)
There is one Human character who was known to be active during the mid 1800s: The Ghost Rider:
- Ghost Rider (aka Phantom Rider) - Born during the mid 1800s, Carter Slade was a schoolteacher who was nearly murdered after a group of cattle ranchers pretended to be Indians and tried to kill families whose land they wanted to take over. He would take on the identity of a masked "Ghost Rider" seeking justice. Carter would eventually die and pass his spiritual essence and powers to his descendants.
More exotic immortals whose stories are partially told but weren't known to have participated directly in the Civil War:
Exodus (Bennet du Paris - Earth-616) An early mutant born in the 12th century whose immortality and vast psionic powers lead him to believe the ultimate fate of humanity was to be replaced by mutants like himself. Lead a group of immortal mutants who called themselves the Externals.
Selene Gallio, an immortal sorceress that survived the fall and sinking of Atlantis over 17,000 years ago. She has been active on and off in the Marvel Universe since that time.
Annihilus - the insect overlord would have been alive during the time of the Civil War but would not have had access to Earth during that time. He would break through to Earth when Reed Richards built a portal into the Negative Zone.
Other metahumans groups whose activity during this period might include:
The Inhumans, a subgroup of Humanity altered by the Kree to express metahuman abilities when exposed to select mutagens have a civilization over 10,000 years old.
The Eternals, an offshoot of Homo Sapiens altered by the Celestials, having incredible superhuman abilities including near-immortality, energy manipulation, psychic abilities and superhuman strength. This would also include the Deviants, another related subgroup of Humanity.
Jeb Lee of Apocalypse's Final Horsemen during the Apocalypse Solution was a confederate spy whose Civil War activities caused a tragic event in his life that activated his mutant bio-auditory cancer powers. Jeb Lee would then roam battlefields playing a drum and killing masses of people. Apocalypse then plucks him out of time to serve as a Famine for his Final Horsemen stable. http://vignette1.wikia.nocookie.net/marveldatabase/images/e/e5/Jeb_Lee_(Earth-616)_from_Uncanny_X-Force_Vol_1_2.png