Norman Osborn physically transforming into the Green Goblin in the first episode. Stark contrast to 616-Marvel, but fits in much better with Ultimate Spider-Man a couple decades later. Perhaps Brian Michael Bendis was watching back in the day.
Videoman's second appearance involves a malfunctioning arcade machine giving a complete dweeb the ability to transform into a superpowered alternate self and back. In other words, it's almost the exact same concept as Freakazoid!.
The Sandman's episode ends with him growing to massive size and fighting our heroes at a construction sight. Sound familiar?
On April 2015, in issue 40 of All-New X-Men Iceman is "outed" as being gay, so seeing Iceman having a romantic infatuation with Firestar on the show could be seen as this.
More Popular Spin-off - On purpose. Amazing Friends came about after a 26-episode Spider-Man series (which was actually quite good, for what it's worth) produced largely to get the big networks' attention. It worked.
Narm Charm - Makes the "Swarm" episode one of the greatest things produced by man. "SWAAAAAAAAAARRRRRRRMMMMMMMM!"
Juggernaut might count for some as well. Most of the episode consists of him doing his Implacable Man impression, wading through everything the heroes throw at him, even when Firestar, the last thing standing between the Juggernaut and his target Prof. X, created a wall of fire to stop him. The Juggernaut walks right into the fire, creating this large silhouette in the flame as his voice echoes, "I'M COMING FOR YOU, CHARLES XAVIER!" The utter look of fear and helplessness on Prof. X's face as the Juggernaut gets closer really sells it, and if Spider-Man hadn't pulled the Professor out of the way at the last second, they make it clear that the Juggernaut would have carried out his threat and killed Charles right there.
The episode in which Videoman appears and have Ice Man and other guy (can't remember who, sorry) trapped in a videogame knowing that when the plug is pulled out they'll vanish totally from existence.
Villain Decay: Dr. Doom, especially in comparison to the previous Spider-Man cartoon in which he was the Big Bad.