Red Skull and Zemo are the big ones. Both are Hydra, though they have pretty different world-views. It's not really their powers that matter, since they're more likely to use wits and carefully crafted plans to get their way.
Zola's an evil scientist who experiments on people
Baron Strucker and Madam Hydra are other Hydra leaders
Crossbones and Batroc are talented mercs, so they usually act in supporting villain roles or as the "mini-bosses".
Aleksander Lukin's a soviet strategist, another chess-master kind of villain, who works from behind the scenes.
Serpent Squad/Society is a terrorist organization.
There are also a number of villains that moved to Captain America comics from other books, like Nuke.
I also like Baron Blood, who is a vampire, but I have no idea when was the last time he was used.