Captain America was recently revealed as a sleeper agent for the terrorist organization Hydra (although why he became one is an interesting story in and of itself). However, he's certainly not the only notable Marvel character to ever to double-duty as a Hydra operative.
Here are the 10 most notable, not only in comics but also on television and in film:
10 Contessa Valentina Allegra de Fontaine
Until the Captain America revelation, likely the most shocking double-agent revelation was Contessa Valentina Allegra de Fontaine, who was introduced by Jim Steranko in 1967's "Strange Tales" #159 and soon became Nick Fury's lover. A character so hot that Marvel constantly edited Steranko's work to tone down her sexuality, the Contessa was a mainstay in S.H.I.E.L.D. comics, mostly as Fury's love interest but also as a major member of the organization in her own right, especially when Fury was off on rogue missions.
During Jonathan Hickman's "Secret Warriors," however, the Contessa revealed herself to be working for Hydra the whole time (specifically for the Russian group, Leviathon). She even became the new Madame Hydra. Fury never got over her, though, even trying to spring her from prison following her capture.
During "Secret Invasion," Nick Fury revealed he'd been keeping tabs on a number of young super-powered individuals who were the offspring of superheroes and supervillains. He then drew them together to help stop the Skrull invasion. After the shape-shifting aliens were repelled, Fury kept the team together (they appeared in "Secret Warriors," but I'm unsure whether they were ever officially given that name).
One of the members of the group was Hellfire, aka J.T. Slade, the grandson of the Phantom Rider, who was able to charge up objects with fire, which he would then use to attack. Ultimately, he was revealed to be secretly working for Hydra, and Baron Von Strucker in particular. Fury let him fall to his death after conceding he knew of Hellfire's betrayal.
Hardball's career as a double agent was mostly one of unfortunate coincidences. In exchange for receiving his superhuman abilities, he had to work for the Power Broker, beginning with the robbery of an armored truck. However, when Hardball attacked, it was just as the truck was about it hit a child. Witnessing the event, Wonder Man presumed Hardball was a good guy, and quickly enlisted him for the Fifty State Initiative, implemented in the wake of "Civil War" to establish a superhero team in each state.
As part of that program, Hardball suddenly became appealing to other villains, so Power Broker sold his contract to Hydra, who used him as a double agent. He eventually became part of the Nevada team the Heavy Hitters - that is until that truth came to light, and he officially joined Hydra. Amusingly enough, he briefly dated the hero Scorpion, who had seemingly also become a Hydra double agent (but she was secretly working undercover for S.H.I.E.L.D.).
7 S.H.I.E.L.D. Super Agents
In "Captain America" #217, we were introduced to the S.H.I.E.L.D. Super Agents, operatives with superpowers. One of those agents, Wendell Vaughn, would go on to become the hero Quasar. However, two of the five members turned out to be working for the evil organization the Conglomerate. So the team broke up after just one mission.
We mention this because, hilariously enough, years later they tried again, introducing a new group of S.H.I.E.L.D. Super Agents in "Nick Fury, Agent of S.H.I.E.L.D." #33: super-strong Knockabout, the Vibranium-infused Ivory, weapons expert Violence and telepath Psi-Borg. We say hilariously because this team also turned out to be double agents! This time, however, they worked for Hydra.
Of the four members, only Ivory wasn't a Hydra operative. She discovered her teammates' true motives, but was killed before she could tell anyone else. Fury took them all out, remarking he was disappointed he hadn't train them well enough to stop him.
6 Silver Fox
Silver Fox is one of the rare characters introduced after she was (supposedly) already dead. She first showed up in "Wolverine" #10 as a reminder that Sabretooth had been tormenting Wolverine for years, including killing Wolverine's girlfriend Silver Fox. However, later on, Larry Hama revealed that Wolverine's memory implants had blinded him to the truth about Silver Fox: She was actually part of a strike force with Wolverine, Sabretooth and Maverick following their time in Weapon X.
However, when she showed up alive years later, Sabretooth seemed surprised to see her, suggesting his memory wasn't all that solid, either. Besides seeing his dead girlfriend alive, Wolverine was also shocked to learn Silver Fox was also a Hydra operative.
Spider-Woman is a fascinating case for this list, because all of her origins -- both her original and more recent ones -- involve her being part of Hydra early in her career (the organization trained her to be an assassin). However, there are some differences as to whether Spider-Woman received her powers from Hydra.
In any event, years later, after she had retired as Spider-Woman due to the loss of her powers, Jessica Drew worked for S.H.I.E.L.D. She was approached by a Hydra agent, who offered to restore her abilities if she spied on S.H.I.E.L.D. Jessica agreed, but then turned out to be a triple agent who reported back to Nick Fury. However, the Hydra cell was actually a group of Skrulls that had replaced Jessica with the Skrull Queen. So now the question is, was the Skrull Queen ever working for Hydra? Seems unlikely, but it is possible!
4 Alexander Pierce
In "Captain America: The Winter Soldier," S.H.I.E.L.D. is overseen by the World Security Council, whose most powerful member is Alexander Pierce (played by Robert Redford), the U.S. Secretary of Defense and an old comrade of Nick Fury. Although Pierce always seemed to protect Fury and S.H.I.E.L.D., in reality he had been working for Hydra.
Pierce hatched a plan to implement a system in which Helicarriers would target for mass assassination anyone who might one day become a threat to Hydra (including pretty much all superhumans). There was a large contingent of Hydra secretly working inside of S.H.I.E.L.D., Pierce was their leader. Fury and his allies reveal Pierce's scheme to the world, and Fury killed his old friend.
Played in "Captain America: The Winter Soldier" by Frank Grillo, Brock Rumlow was a highly decorated S.H.I.E.L.D. agent introduced as part of the black-ops team, Strike (effectively S.H.I.E.L.D.'s answer to Delta Force). However, he's revealed to also be part of the Hydra infiltration.
Rumlow and his Strike team actually managed to capture Captain America and Black Widow. But in the end, the heroes won, and after a long battle between Rumlow and the Falcon, one of Pierce's Helicarriers crashed into the room in the Triskelion where they were fighting. Falcon was able to fly away, but Rumlow was not as lucky. Badly burned, he managed to survive and return to fight again in "Captain America: Civil War," now going by the name Crossbones (with a mask to cover his burned face).
2 John Garrett
John Garrett, played on "Marvel's Agents of S.H.I.E.L.D." by Bill Paxton, was a brilliant operative who turned traitor after he was badly injured on a mission and the organization wouldn't risk sending a medivac helicopter for him. He then offered his services to Hydra.
Unlike some of the people on this list, however, Garrett was no fanatic. He just went where he felt would best serve his purposes. He used his high-level security clearance to access enough documents that he was able to seemingly tell the future, so he created a persona for himself called The Clairvoyant. He had earlier turned his trainee Grant Ward into a loyal member of Hydra, and so he struck against Phil Coulson's select S.H.I.E.L.D. team. Even after seemingly being killed, Garrett briefly came back using Deathlok cyborg technology, but Coulson quickly killed him again.
1 Grant Ward
Played by Brett Dalton, Grant Ward is a unique character on this list, as he's the only one who was a Hydra double agent in the comics as well as on television. Introduced on "Agents of S.H.I.E.L.D.," Ward was a member of Phil Coulson's select group of S.H.I.E.L.D. operatives. He was Coulson's main field operative, as he was a skilled assassin and hand-to-hand combatant. However, it was revealed he had been indoctrinated in the ways of Hydra by John Garrett years earlier.
Unlike Garrett, however, Ward was loyal to Hydra. He ultimately gave his life on a mission to another planet where he was killed and then possessed by the evil being known as Hive. In the comics, Ward was also a S.H.I.E.L.D. agent, only there he was a contemporary of Coulson who was wooed by Hydra.