The Falcon is similar to James Rhodes, in that he was close friends with Tony and was initially intended to pilot the War Machine armor before deciding on the Falcon suit instead (he is also voiced by Bumper Robinson, War Machine's voice actor in Earth's Mightiest Heroes). Additionally, in season 4, he becomes a fusion of different versions of himself as a Plot-Relevant Age-Up saw him trade his classic!Falcon inspired costumes in for one inspired by his MCU and Ultimate counterpart. Furthermore, related to Ultimate, his alternate self in "Planet Doom" wore a costume similar to his Ultimate costume.
M.O.D.O.K. has elements of the movie version of Arnim Zola, mainly his role as the Red Skull's chief scientist. MODOK later merges with the Super-Adaptoid, a completely unrelated character in the original comics. This also means he's got a humanoid robot body with his face appearing on its chest, cementing the Zola connection, however, Zola turns up later on anyway.
The Midgard Serpent is given elements of Cul, Odin's brother from Fear Itself, specifically like him, the Serpent is prophesied to kill Thor. (Although strictly speaking, Cul is decomposited from the Midgard Serpent in Norse Mythology.)
Hyperion is merged with The Sentry and King Hyperion from Exiles. He has the alien fortress of the former and genocidal/megalomanical tendencies of the latter. In fact, The Squadron Supreme are essentially the Squadron Sinister, a similar team of characters who predated the heroes. In particular, their speedster is called Speed Demon rather than Whizzer or Blur - this is the current identity of the Sinisters' Whizzer. They also have versions of Power Princess and Nuke, which the Sinisters never had. At their worst, the Squadron were Well Intentioned Extremists and Nighthawk left to protest their actions. Additionally, Doctor Spectrum is the Billy Roberts version, but is black like the original Kenji Obatu version. This combination of Squadrons was recently brought into canon post-Secret Empire in the form of a Squadron Supreme created by Mephisto.
The show's version of Dracula has elements of Baron Blood, such as his connections to Captain America and World War 2.
The Alternate Timeline version of The Defenders has a Darker and Edgier version of Hawkeye who calls himself Bullseye (after the Daredevil villain, who impersonated Hawkeye whilst a member of the Dark Avengers), and an evil version of Black Widow who acts and dresses exactly like Madame Masque (who later appeared in the final two seasons). The former also wore the costume he wore in The Ultimates 3. Speaking of Hawkeye, in the comics, his mentor (and brother) was an archer called Trick Shot. In the show, Trick Shot was the identity Hawkeye used back when he was a criminal.
Ant-Man is Scott Lang, but has the personality and science background of Hank Pym. The creators said they specifically designed the character to be a composite of the various Ant-Men from the comics.
Radioactive Man is the Russian Igor Stancheck version, but sports the costume and personality of Chen Lu, the original Radioactive Man from China.
A Composite Artifact: In the episode "Beneath the Surface" the animated version of the Serpent Crown functions more like the Horn of Proteus. The comicbook Crown is a source of mind-control powers and other abilities including illusions and energy blasts; the animated Crown, like the comicbook Horn, is used to control Giganto.
Truman Marsh is an all but In Name Only adaptation of the character, with his personality and relationship with the Avengers taken directly from Henry Peter Gyrich. It's also later revealed that Marsh is actually Ultron in disguise.
Baron Mordo is an unambiguous villain and sports his classic costume from the comics, but is also black like his MCU counterpart.
In Avengers: Secret Wars, Thunderstrike is Jane Foster instead of Eric Masterson, allowing a riff on Jane's time as Thor without losing the original Thor.
In Black Panther's Quest, Attuma is given a number of similarities to Namor, the traditional ruler of Atlantis from the comics. In addition to inheriting much of Namor's arrogant personality and his dynamic with Black Panther, Attuma even sports a black ponytail like the one Namor had in the 90s.