In the pilot, Peggy disguised herself with the long blonde hair look she originally had in the comics. Additionally, the voice actress playing her in the "Captain America Adventure Hour" is also blonde.
Leet Brannis shares his name with a minor comics crook from the 40s, an enemy of the Whizzer.
Dottie claims she's training to be a ballerina. In the comics, Black Widows were implanted with false memories of being ballerinas.
"Junior" Juniper is the comics is best known for being the first Marvel hero to be Killed Off for Real. Sure enough, Junior's dead by the end of the episode.
"Happy" Sam Sawyer takes his name from the company commander of the Howling Commandoes in the comics.
When trying to come up with a Howling Commando-style nickname for Peggy, Dugan suggests she call herself "Miss Union Jack." In the comics, Union Jack is a British legacy hero, and all three of the men who used the identity have been close friends and staunch allies of Captain America. James Montgomery Falsworth, the British Howling Commando from Captain America: The First Avenger, was the WWI-era Union Jack in the comics.