Most of Terry's Rogues Gallery is made up of Expies of Spider-Man villains, including Stalker (Kraven the Hunter), Shriek (Shocker with the name and color scheme of Shriek, a recurring Spidey villain with similar powers), and Spellbinder (Mysterio, with the name and color scheme an obscure Silver Age Batman villain, who is also a Mysterio Expy himself). And let's not forget Inque (Venom, and alien symbiotes in general). note Just try watching her introductory scene and not get a Venom symbiote vibe. The animators had fun lampshading this one, as her debut episode has a scene depicting her with two white spots on her face (she has a single one the rest of the time) that make her look remarkably like Spider-Man in his symbiote costume. And just after that scene, she makes a symbiote-esque claw, forms and throws spikes that look identical to Carnage's (except black), and turns her arms into spiky bladed weapons, reminiscent of Carnage. Then her second appearance had her wrapping herself around another person like the symbiote, and making a Venom-like tongue. In a number of issues from the tie in comic (which was written by one of the show's writers), she even displays the symbiotes' ability to take control of people's bodies by wrapping themselves around them! Lastly, her weaknesses are based on the symbiotes' weakness (fire), except that they're the opposite (contact with water, and getting frozen).
An amoral businessman whose experiments turn him into a deranged, green-colored supervillain and Arch-Enemy to a teenage crime fighter. Are we talking about Derek Powers or Norman Osborn?
Willie Watt shares a few similarities to Dr. Octopus, being a gifted scientist with deadly technology at his hands, who had an abusive father; he even has the same hairstyle.
Besides being an analog for Clayface, Inque bares more than a few similarities to Marvel's Mystique, as both are blue-skinned shapeshifting Femme Fatale, complete with difficult relations to their estranged children.
While there is in fact a Spellbinder in the Batman comics (four of them in fact), this guy—an evil psychologist and illusionist who is a bit of a wimp underneath the mask—is most likely the Beyond version of The Scarecrow. He also shares similarities with the Spider-Man villain, Mysterio.
The Stalker is an Egomaniac Hunter who wants to battle a masked superhero in the city? It sounds an awful lot like Spider-Man's Kraven the Hunter.
Kobra, despite being based on an organization from the comics, was made an expy of Cobra-La from G.I. Joe: A Real American Hero in the show. Its leader, original character Zander, is an expy of Serpentor.
Which is even more amusing, as GI Joe and Cobra were themselves expies of Marvel's SHIELD and Hydra. Hasbro asked Marvel to make backstories for their GI Joe toys, and Marvel basically pulled a rejected comic about the son of Nick Fury out of the trash can and changed the names.
Zander is exceedingly similar to Serpentor, the genetically engineered leader of Cobra from GI Joe.
Minor subtle example. Dr. Howard Hodges's jealous rivalry with Mike Morgan brings to mind that of Victor von Doom's with Reed Richards.
Being a sadistic prison warden toward his charges, along with his obsession with punishing people he thinks are responsible for society's moral failing and coddled for their crimes. Dr. David Wheeler slightly resembles a more mundane version of Lyle Bolton/Lock-Up from the original Batman: The Animated Series.
