Your Spoiler-Filled Guide to All the Easter Eggs in Captain America: Civil War

First, the obvious: the title and the premise come from a 2006-2007 Marvel mega-crossover called, appropriately enough, Civil War. In that book, Stamford, Connecticut was destroyed during a super-battle between B-list super-team the New Warriors and B-list villain Nuklon. As a result, the Superhuman Registration Act is passed, mandating the unmasking, registration, and oversight of anyone with any powers of any kind.
The battle lines were similar: Iron Man on the pro-government side, with Captain America making the case for individual liberties. The movie’s equivalent, the Sokovia Accords, are much less far-reaching, in that they only apply to the Avengers, and don’t have anything to do with secret identities—mostly because that’s not really a thing in the Marvel Cinematic Universe.
The outcomes are rather different: in the comics, Iron Man essentially wins when Steve surrenders after a brutal battle in New York City (which is a place you should not live if you happen to call the Marvel U home). Heroes all over the country are registered as part of a Fifty-State Initiative to create registered super-teams in each state, and Tony becomes the director of S.H.I.E.L.D. Oh, and Captain America is shot dead on the way to his arraignment.
Crossbones
The terrorist bad guy from the movie’s opening is Brock Rumlow, better known as Crossbones. A long-time Cap foe (Cap-versary?), we last saw him in the movie version in The Winter Soldier. He’s the S.H.I.E.L.D. agent who was ultimately revealed to be part of Hydra’s master plan. In the comics, he carried out the assassination of Steve Rogers that came about following the Civil War, but he wasn’t alone…
Agent 13

Secret Agent Sharon was introduced as a love interest for Cap way back in 1966, at that time depicted as the much younger sister of Steve’s WWII sweetheart Peggy Carter. More recently, she was portrayed as the original Agent Carter’s niece—still a bit of a stretch given the 50+ year age difference between the two, but comics. On the page, Peggy passed in 2011, shortly after Sharon was brainwashed into shooting Captain America dead on courthouse steps in the postscript to the Civil War miniseries. (Don’t worry, he got better. Before he got old, and then better again.) The story lead into an extended period during which Bucky Barnes, The Winter Soldier, took over as a new Captain America, with the Black Widow and Falcon as his primary sidekicks. If the super-soldier serum in Cap’s blood continues to keep him unnaturally youthful, it’s entirely possible that we’ll get to see him court a third, fourth, maybe even fifth generation of Carters.
Underoos!

As in the movie, Spidey played a critical role in Civil War on the page. He was one of Tony’s most enthusiastic recruits, and, as in the movie, receives a variety of tech upgrades as a result. He even goes so far as to unmask on television, revealing to the world that Spider-Man is actually brainy nebbish Peter Parker. Unlike the movie, Peter eventually turns on Tony (a la Black Widow) when Iron Man goes to far by creating a cyborg clone of the absent Thor, among other things (man I love comics).
This is the third major film incarnation of the character since 2002’s Sam Raimi directed/Tobey Maquire-starring Spider-Man kicked off a successful trilogy. When Raimi dropped out of directing a fourth film, director Marc Webb took over for a 2012 reboot starring Andrew Garfield. The disappointing box office of 2014’s The Amazing Spider-Man 2 brought a halt to that run of movies, as well as several planned spin-offs. It also opened the door for Marvel Studios to cut a deal with Sony Pictures to allow the use of Spidey in films set in the MCU. Sony still controls the rights to the character on film, but everyone’s working together for now. Tom Holland will play Spidey again in next year’s Spider-Man: Homecoming, which will definitely not/probably not be yet another origin story. 
Seeing Scarlet

Scarlet Witch didn’t have much to do in the Civil War comics, though she was responsible for the Avengers Disassembled storyline that saw the team disbanded when Wanda went insane and her reality-warping powers ran amok. Her mental break came following decades worth of comic soap opera at it’s finest: a romance with the synthezoid Vision (which we definitely see hints of in the film) leads to marriage and ultimately children. The marriage goes south for reasons that would take forever to explain, and then it turns out that the kids weren’t really kids, but projections of Wanda’s magical powers. Imbued with pieces of the soul of Marvel’s stand-in for the devil, Mephisto. Brought to life by a witch. (Comics!) And then she was made to forget about them, until she remembered. And the kids actually seem to be doing OK these days. (Have I mentioned how much I love superhero comics?) The point being: whether on page or screen, Wanda + tragedy =  trouble.
Thunderbolt

William Hurt’s Thaddeus Ross was last seen in the Ed Norton-lead Incredible Hulk film. His appearance in Civil War is a nice bit of continuity with that 2008 movie, the green-headed stepchild of Marvel’s run. Even with a cameo from Robert Downey Jr.’s Tony Stark, the money-saving-but-worthwhile casting switchover from Norton to Mark Ruffalo has rendered that second Marvel film an awkward outlier in Marvel Studio’s otherwise continuity-tight universe. In that film, he was the comics’ traditional version of “Thunderbolt” Ross: a U.S. Army general obsessed with bringing down the Hulk, not to mention the father of Bruce Banner’s girlfriend Betty Ross. He’s experience good fortune offscreen in the meantime, having been promoted to Secretary of State. In the comics, Ross hasn’t done quite so well for himself, eventually becoming an even more aggressive red version of the Hulk.
Black Panther Party

The Black Panther was introduced near the height of Stan Lee and Jack Kirby’s legendary run on Fantastic Four in a noble, if incredibly un-subtle, attempt to bring some diversity to the lily-white Marvel U. The character was introduced in 1966, and the name actually predates the birth of the black nationalist Black Panther party—but only by a few months, and the similarity seems largely to have been a coincidence.
The comic-book and movie versions are, thus-far, fairly similar: he’s the hereditary ruler of the reclusive African nation of Wakanda, generally portrayed as the most technologically advanced nation on the planet (you saw hints of that if you stuck around during the closing credits, which, of course you did—this ain’t your first rodeo). It’s also the world’s primary source of vibranium, the super-strong metal from which Captain America’s shield is made. The role of Black Panther has passed from father to son for generations. The bald woman who’s guarding him? She’s one of the Dora Milaje, fierce warriors who represent the tribes of Wakanda as the king’s personal bodyguards. The Panther’s had a few epic runs over the years, but he’s currently being written by social commentator Ta-Nehisi Coates (Between the World and Me). An much earlier story, the groundbreaking Panther’s Rage, is finally being reprinted later this year, so it’s a good time to be a Black Panther fan.
Are you Team Cap or Team Iron Man?