In Black Widow is a costumed S.H.I.E.L.D. agent who apparently defects to HYDRA, but is really a triple agent reporting directly to Nick Fury. Then he disappears, so she can no longer prove this. That's Spider-Woman's story in New Avengers.
Along those same lines, Mockingbird is given most of Spider-Woman's plot from Secret Invasion, right down to getting kidnapped and replaced by Veranke, the Skrull Queen.
Mockingbird actually was replaced by a Skrull in the comics, but the Skrull that did so is a minion of Veranke named H'rpa. Here, Veranke takes H'rpa's place as the identity of the Skrull impostor replacing Mockingbird.
Nick Fury's Season 1 design is a fusion of his Ultimate and classic designs. He's black like Ultimate Fury, but has a full head of hair with gray temples like the original Furynote He originally had full black hair in the shorts leading up to season one, but Baron Strucker's life absorbing claw turned portions of his hair gray, and also wears the latter's trademark S.H.I.E.L.D. jumpsuit. Upon his return in season 2, he becomes more like his Ultimate self by shaving his head and growing a beard.
Baron Zemo is another one, mixing the first Zemo (fought Cap during World War II and leads Masters of Evil) with his son, the second Zemo (costume and personality, the fact that his face was hideously disfigured due to Captain America's actions, which while something similar happened with the first Zemo, was instead his mask being glued to his face, and his actions with the Masters of Evil include the Siege on Avengers Mansion, a scheme done when Helmut reassembled the Masters of Evil a while after Heinrich's death).
The Enchantress takes the Space Phantom's place as the early villain who frames the Hulk to get the rest of the Avengers to turn against him, leading to his departure.
Viper takes Elektra's place as the villain who kicks off the Secret Invasion storyline after it's revealed she's really a Skrull.
In addition, the Skrull impostor among the Avengers is a composite of the Skrulls who replaced Edwin Jarvis and Hank Pym, replacing neither of them due to Jarvis being depicted as an artificial intelligence and Pym having left the Avengers at the time, he instead replaces Captain America, making him an example of this trope as well.
There is also Hulk, who takes from different versions of himself at different periods of time, mixing his original personality, well-known Savage Hulk and recent Green Scar Hulk, causing him to be a lot smarter and rarely use Hulk Speak.
The New Avengers are basically given the origin story of the Young Avengers, the only difference being that while Kang is the enemy the team unites to face, this time he also is the reason the Avengers disappear (replacing Scarlet Witch's role), and that while the New Avengers roster does consist of Spider-Man, Wolverine, Luke Cage, Iron Fist, and Thing, it also includes War Machine, whom was never part of the New Avengers in the comics. The New Avengers' actual origin story (the team assembles to combat a mass prison break) is given to the regular Avengers at the start of the series (with the prison break being caused by Loki rather than Electro, and instead of this taking place at one prison, the Raft, it takes place at four prisons).
William "Crossfire" Cross is given his cousin Darren Cross's role in Scott Lang's origin story.
While the Red Skull is largely the same as his comic book counterpart, his role of being responsible for Bucky's death via the explosion of a rocket plane ( that is until Captain America touched the Cosmic Cube and (unknowingly) altered reality to make it so Bucky survived the blast of the explosion in the 21st century) resembles that of the first Baron Zemo, while the fact that he is portrayed as the mastermind behind Bucky becoming Winter Soldier resemble that of Aleksander Lukin.
