Below are my theories on which Marvel characters will be on which side during Captain America: Civil War (excluding Iron Man and Captain America, for obvious reasons).
Why: Well, for one he was one of Captain America's first allies when he was driven underground in the comics. And after the events of The Winter Soldier, I doubt that he would fight Cap.
Why: I don't remember seeing Black Widow in the Civil War comics, but I think that, like Falcon, she'll stand by Steve after the events of The Winter Soldier.
Why: Well, I'm really not sure where Hawkeye will fall, if he's even in the movie. I can't remember Hawkeye being in the Civil War comics, much like Black Widow, but if he shows up (and that's a big if, especially since I can't shake this nagging feeling at the back of my mind that Hawkeye won't make it through the Age of Ultron) I don't think he'd fight against Black Widow.
Why: Thor never showed up in the Civil War comics, which is why Tony Stark and Reed Richards created a clone of Thor (but that's another matter entirely). Also, it's expected that, by the end of Avengers: Age of Ultron, Thor will be back on Asgard, preparing for Ragnarok.
Why: Much like Thor, the Hulk wasn't in the original Civil War comics. Also like Thor, the Hulk isn't supposed to be on Earth after the Age of Ultron, due to being shot into space with a rocket (where he might meet a team of people who guard the galaxy in 2017...?)
Why: Okay, this one might leave you guys scratching your heads, but just think about it for a second. In the comics, Iron Man recruited several villains to his side. Most notably, for my point here, at least, were the Spider-Man villains that he sent after Peter when he defected to Cap's team. Now, if Black Panther is standing in for Spider-Man, it stands to reason that he'll start out aiding Stark, then go to Steve's team. With that same logic, it makes sense that Stark would send somebody like Klaw to hunt down Black Panther after he leaves. I'm not trying to guarantee that he'll be in the movie; it's just my thoughts on the matter.
Side: Pro, then Anti-Registration
Why: As I said above, it appears that Black Panther will be standing in for Spider-Man and will therefore start out supporting Iron Man and then go over to Captain America's side.
The Winter Soldier
Why: Much like Hawkeye, I'm not sure if the Winter Soldier will join Cap's team. I am, however, 99.999% certain that the Winter Soldier will show up. In fact, he might even save Black Panther from Klaw the same way the the Punisher saved Spider-Man from the villains that Stark sent after him.
Why: In the comics, Daredevil was an ally of Captain America and will be a fully established character, thanks to his soon-to-be show on Netflix. As a totally unnecessary side note, many people have commented on how Daredevil's Netflix costume (as seen in the above picture) doesn't really look anything like his costume in the comics. Maybe Captain America will give it to him when he gets recruited.
The Other Defenders
Why: Well, I don't really know if they'll show up. *shrugs* As I'm sure the above picture indicates, by the other Defenders, I'm referring to Luke Cage, the Iron Fist, and Jessica Jones. Of course, these three characters have their own Marvel shows lined up for Netflix, leading up to a Defenders show. I heard that they will be popping up in each other's shows. Should this be the case, these 'other Defenders' will have already been (slightly) introduced to the MCU. And popping up in Captain America: Civil War will be a great advertisement for them.
And finally...Quicksilver/Scarlet Witch
Why: Much like Hawkeye, the twins haven't been confirmed for Captain America: Civil War. Quite honestly, I highly, highly doubt that they will even show up in the movie at all. Much like Thor and the Hulk, I simply added the twins to cover all of my bases.
So, that's my list. What do you guys think? Did I leave anything out? Anything you'd like to add in the comments?