Squidbillies cartoon and The Gunhawks comics from the early 70s. Keith Harris mentioned Les Tuniques Bleues or The Bluecoats a Belgian comic series now bring published in English about a year ago, based on my suggestion. In each, the authors and artists join forces to discuss the Civil War. Though a kids cartoon, the Squidbillies brilliantly mocks the commercialism surrounding Confederate heritage. The Gunhawks purports to show biracial cooperation between a master's son and a slave during the war and afterwards, a difficult thing to believe. The Bluecoats follows the antics of two Union soldiers, one dedicated and the other malingering, through the war.
I found another that takes a different approach to the topic: Captain Confederacy. Written by Will Shetterly and drawn by Vince Stone, the alternate-reality comic first appeared in 1986. The plot of the first installment, "The Nature of the Hero," follows a fake super hero, Captain Confederacy, and his white female sidekick Miss Dixie, aka the Dixie Duo. The Captain aims to uphold "justice and the Confederate Way" - meaning paternalism towards African Americans, and the independent slaveholding republic (North America is divided into several countries, including the US, the CS, Mormon-led Deseret, the People's Republic of California, Pacifica, Indian-led Great Spirit Land, Republic of Texas, and the Free State of Louisiana). The Captain, however, suffers a crisis of conscience when he discovers that he is a tool for government propaganda. Merely an actor who received the Ultimate Potential serum, his sole job is to maintain the status quo. His nemesis, Blacksnake (!!!) is also an actor named Aaron Jackson. He is exposed as fraud and eventually becomes a rebel to the Confederacy. In the end, the Captain is forgotten and replaced by a new duo, Kid Dixie and a new Captain.
Shetterly produced two other volumes, "Yankee UFO" and "Hero Worship" but neither are as erudite as "The Nature of the Hero" in discussing the war.
Captain Confederacy strikes me as a commentary on the Civil War, racism, gender and the superhero genre. As an alternate-reality idea, it shows what the Confederacy was: a lie. It was based on a stern, conservative, patriarchal system that resisted change. Whites and blacks, men and women - as well as a half-Chinese, half-white character named Lee to mess with the narrative - had their places, and one could not stray from those roles. He and Miss Dixie represent the ideal Confederate (white) man and (white) woman - one strong and virile, the other feminine yet submissive. Blacks are expected to accept white rule for their own good. Two black characters, Aaron Jackson (whose father is the 'richest Tom' in the CSA) and Kate Williams, struggle against the system. Captain Confederacy is forced to reject the system he symbolized. Readers should call him the anti-Superman - he derives his power from a drug, his reputation exposed as a government plot, and his worst enemy is himself. In this sense, Captain Confederacy presages the "CSA" documentary by several years. The two argue that slavery and slaveholding lay at the heart of the Confederate experiment.