Harry Osborn becomes (the first) Venom (although the symbiote adopts this name first while briefly possessing Spider-Man, after using Flash Thompson, White Tiger, Nova, and Iron Fist as hosts). In most continuities he becomes the second Green Goblin while Venom is a separate character named Eddie Brock. In the final season, he takes on original identity Patrioteer (inspired by his stint as American Son), but he continues this by bonding to the Anti-Venom symbiote, which also happened to Brock after separating from Venom in the comics.
Norman Osborn eventually becomes the Iron Patriot like he did in the comics, but the armor he wears is actually modeled after the one sported by James "Rhodey" Rhodes in Iron Man 3, not the one Norman had during Dark Reign. Even as the Green Goblin, he's a fusion of the Goblin of the Ultimate comics (he transforms into a hulking monster instead of wearing a costume) and the classic Goblin (using a glider and bombs, both of which here are S.H.I.E.L.D. tech he stole to compliment his suit). Additionally, while his counterpart from Miles Morales's universe is closer to the actual Ultimate Goblin (having similar horns, as well as being pyrokinetic and leaping around as his mode of travel), he has wings similar to the Goblin from Spider-Man 2099
The origin of the Venom Symbiote also comes from Carnage's origin in Ultimate Spider-Man. The only major difference is that in the Ultimate comics, Curt Conners was the one who created the Symbiote from Peter's blood, while in the TV show, it was Doctor Octopus.
Peter Parker becomes the first incarnation of Carnage due to Cletus Kasady's absence.
Electro starts off in his normal Earth-616 form (complete with the classic costume), but transforms into his energy-based Ultimate counterpart after an accident.
The Power Man used is the original Luke Cage version, but his costume is heavily based off that of Victor Alvarez, the modern Power Man.
Hector Ayala, the original White Tiger, is merged with his own father so that he becomes Ava Ayala's dad (he's her older brother in the comics).
Amadeus Cho, companion to The Incredible Hercules, becomes the Iron Spider, an identity used by Peter Parker around the time of Civil War (2006) in the comics (though Peter had worn the armor in two previous episodes).
The Scorpion's ethnicity, backstory and motivation are largely taken from Davos/Steel Serpent, Iron Fist's nemesis.
The Vulture is the original Adrian Toomes version, but in contrast his comic book counterpart (who has no powers and relies on a winged flight suit), is an actual bird mutate like the Jimmy Natale version of the Vulture.
Power Man's parents are named Walter and Amanda Cage in this adaptation, thus making Luke Cage his legal birth name rather than Carl Lucas. They are based of James and Esther Lucas from the comics, but they are given the same back story of Peter Parker's parents, Richard and Mary, from the Ultimate Universe, being SHIELD scientists working on recreating the Super Soldier Serum and supposedly dying in a plane crash, the only difference being they survived. Since it was their research that gave Luke his powers, they also have elements of Noah Burstein.
Scarlet Spider is a combination of both Scarlet Spiders, having Kaine's costume and personality, but being given the name Ben Reilly by Aunt May. However, he's also a Decomposite Character, as he isn't the Kaine of this universe, who's a separate clone.
In "Return to the Spider-Verse", the role of the Inheritors from the comic book Spider-Verse is taken by Wolf Spider, an evil alternate Peter Parker. There's also a Spider-Gwen who wasn't bitten by a radioactive spider, but duplicates the powers with technology, like a non-steampunk version of May Reilly/Lady Spider of Earth-803 in the comics and additionally, fused with Ultimate!Gwen as this Spider-Gwen hails from the same universe as Miles. Blood Spider is also an alternate version of Peter Parker, as opposed to the comics, where he was a mercenary named Michael Bingham.
The show's version of Spider-Woman turns out to be Mary Jane Watson. Who as Carnage Queen also had elements of Adriana Soria/Spider-Queen and Ultimate Gwen Stacy Clone/Carnage II.
In the final episode, Crossbones is transformed into the new Lizard when Curt Connors is cured.
Mysterio is Francine Beck, daughter of Quentin Beck. The character is loosely based on Maguire Beck, a cousin of Quentin's who wanted to avenge his death, but who used the Jack O'Lantern identity to do it, teaming up with her cousin's apprentice Daniel Beckhart as the new Mysterio. The "Francine" name appears to come from Francis Klum, who briefly took the Mysterio name at around the same time and was challenged by Daniel.
In the "Spider-Slayers" arc, the Slayers have elements of the Spider-Clones (especially the "Maximum Clonage" and "Ultimate Clone Saga" versions, which had more variants than "duplicate Spider-Man") and Deathweb, a team of spider-themed villains that fought the West Coast Avengers and included a huge guy (Therak) and a white-clad teleporter (Anthro). The name comes from Spencer Smythe's anti-spider robots in the comics.
